Starting phenix.real_space_refine on Tue Jun 24 12:34:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkq_34858/06_2025/8hkq_34858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkq_34858/06_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_34858/06_2025/8hkq_34858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkq_34858/06_2025/8hkq_34858.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkq_34858/06_2025/8hkq_34858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkq_34858/06_2025/8hkq_34858.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.035 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): 0.88s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} 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: 18.87, per 1000 atoms: 0.66 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: 7.58 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.75 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: 11.76 Time building geometry restraints manager: 8.81 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) selection = (chain 'B' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) selection = (chain 'C' and (resid 110 through 1205 or resid 1301 through 1302 or resid 1304 \ through 1305)) selection = (chain 'D' and (resid 110 through 1205 or resid 1301 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 74.370 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.140 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.650 ------------------------------------------------------------------------------- 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 : 8.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.048 0.002 TRP C 325 HIS 0.005 0.001 HIS C 291 PHE 0.030 0.001 PHE B 268 TYR 0.019 0.001 TYR D 553 ARG 0.007 0.000 ARG B 600 Details of bonding type rmsd hydrogen bonds : bond 0.15336 ( 1376) hydrogen bonds : angle 5.22912 ( 3876) metal coordination : bond 0.00173 ( 16) metal coordination : angle 0.77524 ( 12) covalent geometry : bond 0.00840 (29340) covalent geometry : angle 0.76163 (39884) *********************** 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 : 5.049 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: 1.2524 time to fit residues: 766.5649 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 : 3.128 ------------------------------------------------------------------------------- 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 303 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 326 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 119 ASN D 218 ASN ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 GLN D 470 GLN D 505 HIS D 632 ASN D 800 ASN A 251 ASN A 254 ASN ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN A 469 HIS A 470 GLN A 505 HIS ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 879 ASN A1159 HIS C 251 ASN C 254 ASN ** C 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN C 470 GLN C 505 HIS C 540 GLN C 603 ASN C 632 ASN C 800 ASN C 816 ASN C1155 ASN C1159 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN B 470 GLN B 484 ASN B 505 HIS B 588 HIS B 632 ASN B 800 ASN B1155 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.109448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087720 restraints weight = 74599.234| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.67 r_work: 0.3353 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29356 Z= 0.247 Angle : 0.832 13.084 39896 Z= 0.411 Chirality : 0.049 0.320 4556 Planarity : 0.006 0.083 5008 Dihedral : 7.473 84.620 3992 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.66 % Allowed : 21.47 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3552 helix: 0.36 (0.12), residues: 1696 sheet: -0.77 (0.27), residues: 344 loop : -0.19 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 243 HIS 0.012 0.002 HIS C 291 PHE 0.075 0.003 PHE C 212 TYR 0.024 0.003 TYR C 987 ARG 0.011 0.001 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 1376) hydrogen bonds : angle 4.62119 ( 3876) metal coordination : bond 0.01148 ( 16) metal coordination : angle 2.01787 ( 12) covalent geometry : bond 0.00568 (29340) covalent geometry : angle 0.83129 (39884) *********************** 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 597 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 453 time to evaluate : 4.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 192 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: D 216 MET cc_start: 0.7573 (tpt) cc_final: 0.6998 (tpp) REVERT: D 340 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8418 (m) REVERT: D 388 ASP cc_start: 0.7687 (t0) cc_final: 0.7372 (t0) REVERT: D 566 MET cc_start: 0.8048 (tmm) cc_final: 0.7587 (tmt) REVERT: D 1010 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8433 (ptm) REVERT: D 1157 MET cc_start: 0.7466 (mtp) cc_final: 0.7168 (mtt) REVERT: A 222 PHE cc_start: 0.8307 (m-80) cc_final: 0.8020 (t80) REVERT: A 473 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 799 LYS cc_start: 0.7834 (pttp) cc_final: 0.7634 (ptmm) REVERT: A 841 LYS cc_start: 0.8171 (tmmt) cc_final: 0.7850 (tmmm) REVERT: A 972 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6699 (mm) REVERT: C 119 ASN cc_start: 0.7110 (t0) cc_final: 0.6837 (t0) REVERT: C 174 MET cc_start: 0.6716 (mmm) cc_final: 0.5775 (pmm) REVERT: C 356 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7445 (ttm170) REVERT: C 844 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6862 (p-80) REVERT: C 1136 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 204 TRP cc_start: 0.5317 (t-100) cc_final: 0.5026 (t60) REVERT: B 216 MET cc_start: 0.8013 (ttp) cc_final: 0.7215 (tpp) REVERT: B 222 PHE cc_start: 0.8306 (m-80) cc_final: 0.7751 (t80) REVERT: B 389 PHE cc_start: 0.7925 (t80) cc_final: 0.7420 (t80) REVERT: B 930 MET cc_start: 0.5763 (tpt) cc_final: 0.5547 (tpt) REVERT: B 1011 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7873 (ttmt) REVERT: B 1162 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7230 (mt) outliers start: 144 outliers final: 24 residues processed: 548 average time/residue: 1.2237 time to fit residues: 822.7736 Evaluate side-chains 379 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 345 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 917 ILE 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 356 ARG 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 844 HIS Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 119 optimal weight: 0.7980 chunk 199 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 342 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 178 optimal weight: 0.0270 chunk 314 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 HIS D 879 ASN ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 460 ASN A 548 GLN A1159 HIS C 180 GLN C 469 HIS C 879 ASN C1159 HIS B 460 ASN B 469 HIS B 879 ASN B1159 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082837 restraints weight = 74529.894| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.69 r_work: 0.3320 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29356 Z= 0.135 Angle : 0.624 10.433 39896 Z= 0.300 Chirality : 0.042 0.201 4556 Planarity : 0.004 0.083 5008 Dihedral : 6.962 86.658 3986 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.40 % Allowed : 24.94 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3552 helix: 0.74 (0.13), residues: 1740 sheet: -0.83 (0.27), residues: 368 loop : -0.02 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 325 HIS 0.010 0.001 HIS C1159 PHE 0.044 0.002 PHE C 212 TYR 0.026 0.001 TYR C 317 ARG 0.007 0.000 ARG C 418 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1376) hydrogen bonds : angle 4.30743 ( 3876) metal coordination : bond 0.00269 ( 16) metal coordination : angle 1.29559 ( 12) covalent geometry : bond 0.00309 (29340) covalent geometry : angle 0.62390 (39884) *********************** 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 478 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 373 time to evaluate : 2.983 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: 0.7559 (tpt) cc_final: 0.7202 (tpp) REVERT: D 545 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.7153 (p) REVERT: D 566 MET cc_start: 0.8219 (tmm) cc_final: 0.7792 (tmt) REVERT: D 1157 MET cc_start: 0.7544 (mtp) cc_final: 0.7222 (mtt) REVERT: A 127 CYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 222 PHE cc_start: 0.8277 (m-80) cc_final: 0.8056 (t80) REVERT: A 356 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7431 (ppp80) REVERT: A 415 GLN cc_start: 0.8273 (mp-120) cc_final: 0.8031 (mp-120) REVERT: A 447 MET cc_start: 0.8249 (mmm) cc_final: 0.8018 (mmm) REVERT: A 473 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8586 (mp) REVERT: A 566 MET cc_start: 0.6558 (tpp) cc_final: 0.6343 (tmm) REVERT: A 799 LYS cc_start: 0.8128 (pttp) cc_final: 0.7823 (ptmm) REVERT: A 896 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.6636 (mpt) REVERT: A 972 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6965 (mm) REVERT: C 119 ASN cc_start: 0.7208 (t0) cc_final: 0.6874 (t0) REVERT: C 276 CYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8145 (t) REVERT: C 292 LEU cc_start: 0.8588 (tp) cc_final: 0.8379 (tp) REVERT: C 356 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7467 (ttm170) REVERT: C 631 GLU cc_start: 0.7549 (mp0) cc_final: 0.7278 (mp0) REVERT: C 844 HIS cc_start: 0.7187 (OUTLIER) cc_final: 0.6973 (p-80) REVERT: C 1157 MET cc_start: 0.8107 (mtp) cc_final: 0.7897 (mtp) REVERT: B 129 LEU cc_start: 0.8812 (tp) cc_final: 0.8605 (tm) REVERT: B 188 PHE cc_start: 0.8345 (t80) cc_final: 0.7831 (t80) REVERT: B 204 TRP cc_start: 0.5335 (t-100) cc_final: 0.5059 (t60) REVERT: B 216 MET cc_start: 0.7947 (ttp) cc_final: 0.7260 (tpp) REVERT: B 222 PHE cc_start: 0.8564 (m-80) cc_final: 0.8043 (t80) REVERT: B 465 THR cc_start: 0.8883 (t) cc_final: 0.8655 (m) REVERT: B 565 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7271 (ptm-80) REVERT: B 1010 MET cc_start: 0.8414 (ppp) cc_final: 0.8195 (ptt) REVERT: B 1011 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8071 (tppt) REVERT: B 1162 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7438 (mt) outliers start: 105 outliers final: 39 residues processed: 444 average time/residue: 1.1097 time to fit residues: 604.6403 Evaluate side-chains 376 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 325 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 844 HIS Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 299 LEU 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 473 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 925 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 62 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 257 optimal weight: 0.0000 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 0.1980 chunk 203 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 981 GLN D1159 HIS A1159 HIS C 180 GLN C1159 HIS B 119 ASN B 218 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.104961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082341 restraints weight = 74438.117| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.85 r_work: 0.3264 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29356 Z= 0.148 Angle : 0.621 10.938 39896 Z= 0.300 Chirality : 0.042 0.182 4556 Planarity : 0.004 0.081 5008 Dihedral : 6.517 81.576 3986 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.95 % Allowed : 24.87 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3552 helix: 0.95 (0.13), residues: 1708 sheet: -0.78 (0.27), residues: 368 loop : 0.25 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 325 HIS 0.028 0.001 HIS B 291 PHE 0.049 0.002 PHE A 212 TYR 0.022 0.002 TYR B 351 ARG 0.010 0.000 ARG D 948 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1376) hydrogen bonds : angle 4.20745 ( 3876) metal coordination : bond 0.00508 ( 16) metal coordination : angle 1.38529 ( 12) covalent geometry : bond 0.00350 (29340) covalent geometry : angle 0.62017 (39884) *********************** 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 480 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 358 time to evaluate : 5.332 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: 0.7659 (tpt) cc_final: 0.7339 (tpp) REVERT: D 545 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7715 (p) REVERT: D 566 MET cc_start: 0.8344 (tmm) cc_final: 0.7911 (tmt) REVERT: D 1157 MET cc_start: 0.7596 (mtp) cc_final: 0.7328 (mtt) REVERT: A 127 CYS cc_start: 0.8544 (t) cc_final: 0.8276 (m) REVERT: A 216 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7858 (mmm) REVERT: A 447 MET cc_start: 0.8373 (mmm) cc_final: 0.7975 (tpt) REVERT: A 473 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 516 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: A 799 LYS cc_start: 0.8400 (pttp) cc_final: 0.8156 (ptmm) REVERT: A 896 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.6708 (mpt) REVERT: A 972 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7164 (mm) REVERT: A 1138 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6924 (mm) REVERT: C 174 MET cc_start: 0.6940 (mmm) cc_final: 0.6006 (pmm) REVERT: C 276 CYS cc_start: 0.8466 (m) cc_final: 0.8188 (t) REVERT: C 292 LEU cc_start: 0.8650 (tp) cc_final: 0.8445 (tp) REVERT: C 447 MET cc_start: 0.7975 (mmm) cc_final: 0.7733 (mmm) REVERT: C 516 MET cc_start: 0.8429 (mtm) cc_final: 0.8139 (mtp) REVERT: C 631 GLU cc_start: 0.7708 (mp0) cc_final: 0.7378 (mp0) REVERT: C 844 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.7005 (p-80) REVERT: C 1136 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: C 1157 MET cc_start: 0.8185 (mtp) cc_final: 0.7965 (mtp) REVERT: B 129 LEU cc_start: 0.8824 (tp) cc_final: 0.8527 (tm) REVERT: B 188 PHE cc_start: 0.8375 (t80) cc_final: 0.7803 (t80) REVERT: B 204 TRP cc_start: 0.5485 (t-100) cc_final: 0.5151 (t60) REVERT: B 216 MET cc_start: 0.8049 (ttp) cc_final: 0.7195 (tpp) REVERT: B 220 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7784 (pt) REVERT: B 222 PHE cc_start: 0.8589 (m-80) cc_final: 0.8158 (t80) REVERT: B 351 TYR cc_start: 0.7356 (t80) cc_final: 0.7148 (t80) REVERT: B 372 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7374 (mtmt) REVERT: B 538 ARG cc_start: 0.8540 (mtp85) cc_final: 0.8249 (mtp85) REVERT: B 757 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7893 (m) REVERT: B 828 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7746 (ttm-80) REVERT: B 930 MET cc_start: 0.6529 (tpt) cc_final: 0.6300 (tpt) REVERT: B 938 TYR cc_start: 0.7736 (t80) cc_final: 0.7436 (t80) REVERT: B 1011 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8290 (tppt) outliers start: 122 outliers final: 38 residues processed: 439 average time/residue: 1.5972 time to fit residues: 859.5346 Evaluate side-chains 380 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 379 SER 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 545 SER Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 299 LEU 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 473 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 896 MET 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 170 VAL Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 925 SER 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 1162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 240 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 341 optimal weight: 0.4980 chunk 218 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 266 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN D 844 HIS D 981 GLN D1159 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 981 GLN A1159 HIS C 490 GLN C1159 HIS B 588 HIS B1159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.104486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082629 restraints weight = 73422.660| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.60 r_work: 0.3242 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.6698 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= 0.163 Angle : 0.636 13.011 39896 Z= 0.308 Chirality : 0.043 0.170 4556 Planarity : 0.004 0.080 5008 Dihedral : 6.264 74.926 3984 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.15 % Allowed : 25.03 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3552 helix: 1.05 (0.13), residues: 1700 sheet: -0.79 (0.27), residues: 368 loop : 0.32 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 325 HIS 0.018 0.001 HIS B 291 PHE 0.040 0.002 PHE B 235 TYR 0.014 0.001 TYR B 351 ARG 0.010 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1376) hydrogen bonds : angle 4.21023 ( 3876) metal coordination : bond 0.00331 ( 16) metal coordination : angle 1.21018 ( 12) covalent geometry : bond 0.00384 (29340) covalent geometry : angle 0.63579 (39884) *********************** 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 490 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 362 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7618 (tpt) cc_final: 0.7357 (tpp) REVERT: D 447 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7694 (mmt) REVERT: D 545 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8219 (p) REVERT: D 566 MET cc_start: 0.8341 (tmm) cc_final: 0.7862 (tmt) REVERT: D 1010 MET cc_start: 0.8808 (ptm) cc_final: 0.8512 (ttp) REVERT: D 1017 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8345 (mm) REVERT: D 1157 MET cc_start: 0.7763 (mtp) cc_final: 0.7546 (mtt) REVERT: A 127 CYS cc_start: 0.8532 (t) cc_final: 0.8304 (m) REVERT: A 231 LEU cc_start: 0.8040 (mm) cc_final: 0.7755 (tp) REVERT: A 356 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7635 (ppp80) REVERT: A 447 MET cc_start: 0.8559 (mmm) cc_final: 0.8183 (tpt) REVERT: A 473 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 799 LYS cc_start: 0.8558 (pttp) cc_final: 0.8292 (ptmm) REVERT: A 972 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7243 (mm) REVERT: A 1138 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7192 (mm) REVERT: C 174 MET cc_start: 0.6871 (mmm) cc_final: 0.6006 (pmm) REVERT: C 276 CYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8216 (t) REVERT: C 279 LEU cc_start: 0.8640 (tm) cc_final: 0.8402 (tt) REVERT: C 447 MET cc_start: 0.8147 (mmm) cc_final: 0.7603 (tpp) REVERT: C 631 GLU cc_start: 0.7878 (mp0) cc_final: 0.7555 (mp0) REVERT: C 844 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.7074 (p-80) REVERT: C 930 MET cc_start: 0.7012 (tpt) cc_final: 0.6621 (tpt) REVERT: C 1136 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: C 1157 MET cc_start: 0.8224 (mtp) cc_final: 0.8017 (mtp) REVERT: B 143 ILE cc_start: 0.8103 (pt) cc_final: 0.7698 (pp) REVERT: B 188 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 204 TRP cc_start: 0.5505 (t-100) cc_final: 0.5157 (t60) REVERT: B 216 MET cc_start: 0.8106 (ttp) cc_final: 0.7419 (tpp) REVERT: B 222 PHE cc_start: 0.8649 (m-80) cc_final: 0.8179 (t80) REVERT: B 473 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8477 (mp) REVERT: B 538 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8123 (mtp85) REVERT: B 564 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 757 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 828 ARG cc_start: 0.8040 (ptm160) cc_final: 0.7771 (ttp80) REVERT: B 1011 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8497 (tppt) outliers start: 128 outliers final: 44 residues processed: 444 average time/residue: 1.1933 time to fit residues: 649.5730 Evaluate side-chains 387 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 328 time to evaluate : 2.958 ------------------------------------------------------------------------------- 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 217 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 405 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 545 SER Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 253 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 972 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 405 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 564 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 1011 LYS 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 1162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 192 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 357 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 GLN D1159 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS C1159 HIS B 816 ASN B1159 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.103201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081170 restraints weight = 73646.776| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.61 r_work: 0.3210 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29356 Z= 0.184 Angle : 0.655 14.134 39896 Z= 0.316 Chirality : 0.044 0.228 4556 Planarity : 0.004 0.073 5008 Dihedral : 5.974 63.318 3984 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.31 % Allowed : 25.36 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3552 helix: 1.02 (0.13), residues: 1712 sheet: -0.79 (0.27), residues: 368 loop : 0.38 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 325 HIS 0.026 0.002 HIS A 291 PHE 0.056 0.002 PHE A 235 TYR 0.025 0.002 TYR A1167 ARG 0.013 0.000 ARG D 948 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1376) hydrogen bonds : angle 4.20257 ( 3876) metal coordination : bond 0.00536 ( 16) metal coordination : angle 1.21708 ( 12) covalent geometry : bond 0.00446 (29340) covalent geometry : angle 0.65450 (39884) *********************** 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 492 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 359 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 447 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7941 (mmt) REVERT: D 1017 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 163 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7688 (p0) REVERT: A 231 LEU cc_start: 0.8201 (mm) cc_final: 0.7876 (tp) REVERT: A 352 LEU cc_start: 0.7960 (pp) cc_final: 0.7759 (pp) REVERT: A 356 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7740 (ppp80) REVERT: A 447 MET cc_start: 0.8652 (mmm) cc_final: 0.8350 (tpt) REVERT: A 473 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 799 LYS cc_start: 0.8650 (pttp) cc_final: 0.8290 (ptmm) REVERT: A 841 LYS cc_start: 0.8825 (ttpt) cc_final: 0.8552 (tmmm) REVERT: A 972 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7161 (mm) REVERT: C 119 ASN cc_start: 0.7560 (t0) cc_final: 0.7248 (m-40) REVERT: C 217 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8286 (tp) REVERT: C 276 CYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (t) REVERT: C 279 LEU cc_start: 0.8750 (tm) cc_final: 0.8500 (tt) REVERT: C 351 TYR cc_start: 0.8023 (t80) cc_final: 0.7553 (t80) REVERT: C 356 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7518 (ttm170) REVERT: C 427 GLN cc_start: 0.8369 (pm20) cc_final: 0.8044 (pm20) REVERT: C 447 MET cc_start: 0.8235 (mmm) cc_final: 0.7673 (tpp) REVERT: C 773 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8189 (ptmt) REVERT: C 844 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.7006 (t-90) REVERT: C 930 MET cc_start: 0.7246 (tpt) cc_final: 0.6589 (tpt) REVERT: C 1136 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: B 129 LEU cc_start: 0.8779 (tp) cc_final: 0.8481 (tm) REVERT: B 143 ILE cc_start: 0.8154 (pt) cc_final: 0.7791 (pp) REVERT: B 188 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.6432 (t80) REVERT: B 204 TRP cc_start: 0.5482 (t-100) cc_final: 0.5198 (t60) REVERT: B 216 MET cc_start: 0.8091 (ttp) cc_final: 0.7291 (tpp) REVERT: B 220 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7827 (pt) REVERT: B 222 PHE cc_start: 0.8435 (m-80) cc_final: 0.7867 (t80) REVERT: B 473 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 538 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8164 (mtp85) REVERT: B 564 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 828 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7895 (ttp80) REVERT: B 1011 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8617 (tppt) REVERT: B 1204 LEU cc_start: 0.8283 (mt) cc_final: 0.7949 (mp) outliers start: 133 outliers final: 53 residues processed: 446 average time/residue: 1.3452 time to fit residues: 726.1533 Evaluate side-chains 402 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 333 time to evaluate : 3.031 ------------------------------------------------------------------------------- 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 274 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 379 SER 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 714 LEU Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL 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 325 TRP 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 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 274 LEU 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 356 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 188 PHE 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 234 LEU Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 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 564 ILE Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 1011 LYS 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 1159 HIS 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 253 optimal weight: 0.0270 chunk 348 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 256 optimal weight: 3.9990 chunk 95 optimal weight: 0.0470 chunk 264 optimal weight: 4.9990 chunk 308 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.9938 ------------------------------------------------------------------------------- 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 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS C 490 GLN C1159 HIS B1159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.104455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081561 restraints weight = 72393.584| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.77 r_work: 0.3205 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29356 Z= 0.127 Angle : 0.638 14.190 39896 Z= 0.302 Chirality : 0.042 0.191 4556 Planarity : 0.004 0.075 5008 Dihedral : 5.803 61.015 3984 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.11 % Allowed : 27.49 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3552 helix: 1.13 (0.13), residues: 1716 sheet: -0.72 (0.27), residues: 368 loop : 0.34 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 325 HIS 0.036 0.001 HIS A 291 PHE 0.049 0.002 PHE A 235 TYR 0.026 0.001 TYR A1167 ARG 0.010 0.000 ARG C 418 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 1376) hydrogen bonds : angle 4.15410 ( 3876) metal coordination : bond 0.00423 ( 16) metal coordination : angle 1.15591 ( 12) covalent geometry : bond 0.00292 (29340) covalent geometry : angle 0.63809 (39884) *********************** 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 442 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 346 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7179 (tpp) cc_final: 0.6860 (tpp) REVERT: D 447 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7964 (mmt) REVERT: D 896 MET cc_start: 0.8797 (mmt) cc_final: 0.8460 (mmm) REVERT: D 1017 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 231 LEU cc_start: 0.8005 (mm) cc_final: 0.7771 (tp) REVERT: A 356 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7792 (ppp80) REVERT: A 447 MET cc_start: 0.8652 (mmm) cc_final: 0.8374 (tpt) REVERT: A 473 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 799 LYS cc_start: 0.8689 (pttp) cc_final: 0.8305 (ptmm) REVERT: A 841 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8614 (tmmm) REVERT: A 972 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7039 (mm) REVERT: C 119 ASN cc_start: 0.7609 (t0) cc_final: 0.7309 (m-40) REVERT: C 217 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8116 (tp) REVERT: C 276 CYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8320 (t) REVERT: C 279 LEU cc_start: 0.8754 (tm) cc_final: 0.8506 (tt) REVERT: C 418 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8452 (mtt180) REVERT: C 447 MET cc_start: 0.8263 (mmm) cc_final: 0.7655 (tpp) REVERT: C 773 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8254 (ptmt) REVERT: C 829 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8257 (mttp) REVERT: C 844 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.7083 (t-90) REVERT: C 930 MET cc_start: 0.7172 (tpt) cc_final: 0.6548 (tpt) REVERT: B 143 ILE cc_start: 0.8186 (pt) cc_final: 0.7833 (pp) REVERT: B 174 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7397 (tpp) REVERT: B 204 TRP cc_start: 0.5537 (t-100) cc_final: 0.5230 (t60) REVERT: B 538 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8126 (mtp85) REVERT: B 828 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7939 (ttp80) REVERT: B 930 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6717 (tpt) REVERT: B 1011 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8640 (ttmt) REVERT: B 1138 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7460 (mm) REVERT: B 1141 TYR cc_start: 0.8046 (t80) cc_final: 0.7787 (t80) REVERT: B 1204 LEU cc_start: 0.8285 (mt) cc_final: 0.7964 (mp) outliers start: 96 outliers final: 49 residues processed: 411 average time/residue: 1.1681 time to fit residues: 583.6797 Evaluate side-chains 393 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 332 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 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 274 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 379 SER 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 714 LEU Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 280 CYS 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 627 ILE Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN 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 217 ILE 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 404 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 188 PHE 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 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 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 1162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 0.7980 chunk 335 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 chunk 312 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 247 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 C1159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.104372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081724 restraints weight = 72857.081| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.80 r_work: 0.3200 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7656 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= 0.121 Angle : 0.643 13.912 39896 Z= 0.302 Chirality : 0.042 0.222 4556 Planarity : 0.004 0.063 5008 Dihedral : 5.567 55.557 3984 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.14 % Allowed : 27.62 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3552 helix: 1.16 (0.13), residues: 1724 sheet: -0.63 (0.27), residues: 368 loop : 0.38 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 325 HIS 0.037 0.001 HIS A 291 PHE 0.032 0.001 PHE B 235 TYR 0.025 0.001 TYR A1167 ARG 0.010 0.000 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 1376) hydrogen bonds : angle 4.11721 ( 3876) metal coordination : bond 0.00465 ( 16) metal coordination : angle 1.22782 ( 12) covalent geometry : bond 0.00278 (29340) covalent geometry : angle 0.64272 (39884) *********************** 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 436 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 339 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 PHE cc_start: 0.8184 (t80) cc_final: 0.7631 (m-80) REVERT: D 192 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7384 (mmm) REVERT: D 216 MET cc_start: 0.7271 (tpp) cc_final: 0.6868 (tpp) REVERT: D 447 MET cc_start: 0.8432 (mmm) cc_final: 0.8028 (mmt) REVERT: D 566 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: D 896 MET cc_start: 0.8824 (mmt) cc_final: 0.8446 (mmm) REVERT: D 936 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: D 1017 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 163 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7603 (p0) REVERT: A 192 MET cc_start: 0.7527 (mpm) cc_final: 0.7095 (mpt) REVERT: A 231 LEU cc_start: 0.7998 (mm) cc_final: 0.7738 (tp) REVERT: A 340 VAL cc_start: 0.8902 (p) cc_final: 0.8698 (m) REVERT: A 356 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7824 (ppp80) REVERT: A 447 MET cc_start: 0.8675 (mmm) cc_final: 0.8392 (tpt) REVERT: A 473 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8608 (mp) REVERT: A 799 LYS cc_start: 0.8702 (pttp) cc_final: 0.8300 (ptmm) REVERT: A 841 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8632 (tmmm) REVERT: A 972 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7175 (mm) REVERT: A 1138 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7171 (mm) REVERT: C 119 ASN cc_start: 0.7669 (t0) cc_final: 0.7383 (m-40) REVERT: C 276 CYS cc_start: 0.8603 (m) cc_final: 0.8322 (t) REVERT: C 279 LEU cc_start: 0.8766 (tm) cc_final: 0.8509 (tt) REVERT: C 447 MET cc_start: 0.8292 (mmm) cc_final: 0.7752 (tpp) REVERT: C 773 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8248 (ptmt) REVERT: C 829 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8262 (mttp) REVERT: C 844 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.7078 (t-90) REVERT: C 930 MET cc_start: 0.7160 (tpt) cc_final: 0.6562 (tpt) REVERT: B 143 ILE cc_start: 0.8200 (pt) cc_final: 0.7872 (pp) REVERT: B 204 TRP cc_start: 0.5603 (t-100) cc_final: 0.5272 (t60) REVERT: B 216 MET cc_start: 0.8116 (ttp) cc_final: 0.7649 (tpp) REVERT: B 222 PHE cc_start: 0.8399 (m-80) cc_final: 0.7554 (t80) REVERT: B 236 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8078 (pt) REVERT: B 352 LEU cc_start: 0.8200 (tt) cc_final: 0.7928 (mp) REVERT: B 538 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8082 (mtp85) REVERT: B 564 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8004 (tp) REVERT: B 828 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7962 (ttp80) REVERT: B 930 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6638 (tpt) REVERT: B 1011 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: B 1138 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7395 (mm) REVERT: B 1204 LEU cc_start: 0.8284 (mt) cc_final: 0.7953 (mp) outliers start: 97 outliers final: 50 residues processed: 405 average time/residue: 1.1374 time to fit residues: 559.3281 Evaluate side-chains 390 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 324 time to evaluate : 3.204 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 716 LEU 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 162 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 280 CYS 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 627 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 981 GLN Chi-restraints excluded: chain A residue 1010 MET 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 155 PHE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 188 PHE 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 236 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 787 HIS Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 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 1187 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 85 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 344 optimal weight: 0.7980 chunk 280 optimal weight: 0.0870 chunk 335 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 A1159 HIS ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.103997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081732 restraints weight = 73411.804| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.84 r_work: 0.3192 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29356 Z= 0.117 Angle : 0.649 13.580 39896 Z= 0.304 Chirality : 0.042 0.257 4556 Planarity : 0.004 0.069 5008 Dihedral : 5.395 53.432 3984 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.72 % Allowed : 28.08 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3552 helix: 1.21 (0.13), residues: 1724 sheet: -0.54 (0.28), residues: 368 loop : 0.40 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 325 HIS 0.051 0.002 HIS B 291 PHE 0.040 0.002 PHE A 235 TYR 0.024 0.001 TYR A1167 ARG 0.011 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 1376) hydrogen bonds : angle 4.09011 ( 3876) metal coordination : bond 0.00448 ( 16) metal coordination : angle 1.23640 ( 12) covalent geometry : bond 0.00268 (29340) covalent geometry : angle 0.64841 (39884) *********************** 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 418 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 334 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 PHE cc_start: 0.8217 (t80) cc_final: 0.7623 (m-80) REVERT: D 192 MET cc_start: 0.7638 (mmm) cc_final: 0.7337 (mmm) REVERT: D 216 MET cc_start: 0.7296 (tpp) cc_final: 0.6964 (tpp) REVERT: D 274 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8672 (tp) REVERT: D 306 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7576 (t80) REVERT: D 780 ARG cc_start: 0.8377 (ttt90) cc_final: 0.8125 (ttt-90) REVERT: D 896 MET cc_start: 0.8796 (mmt) cc_final: 0.8389 (mmm) REVERT: D 936 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: D 1017 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8213 (mm) REVERT: D 1157 MET cc_start: 0.7954 (mtp) cc_final: 0.7738 (mtm) REVERT: A 163 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 231 LEU cc_start: 0.7933 (mm) cc_final: 0.7675 (tp) REVERT: A 340 VAL cc_start: 0.8890 (p) cc_final: 0.8673 (m) REVERT: A 356 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7892 (ppp80) REVERT: A 447 MET cc_start: 0.8678 (mmm) cc_final: 0.8388 (tpt) REVERT: A 473 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8608 (mp) REVERT: A 799 LYS cc_start: 0.8703 (pttp) cc_final: 0.8336 (ptmm) REVERT: A 972 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7163 (mm) REVERT: A 1138 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7194 (mm) REVERT: C 119 ASN cc_start: 0.7664 (t0) cc_final: 0.7385 (m-40) REVERT: C 216 MET cc_start: 0.8177 (mmt) cc_final: 0.7295 (pp-130) REVERT: C 276 CYS cc_start: 0.8735 (m) cc_final: 0.8376 (t) REVERT: C 279 LEU cc_start: 0.8734 (tm) cc_final: 0.8477 (tt) REVERT: C 418 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7984 (ttm-80) REVERT: C 447 MET cc_start: 0.8329 (mmm) cc_final: 0.7680 (tpp) REVERT: C 773 LYS cc_start: 0.8526 (mtpt) cc_final: 0.8265 (ptmt) REVERT: C 829 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8273 (mttp) REVERT: C 844 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.7137 (t-90) REVERT: C 930 MET cc_start: 0.7220 (tpt) cc_final: 0.6599 (tpt) REVERT: B 204 TRP cc_start: 0.5638 (t-100) cc_final: 0.5299 (t60) REVERT: B 216 MET cc_start: 0.8171 (ttp) cc_final: 0.7653 (tpp) REVERT: B 222 PHE cc_start: 0.8367 (m-80) cc_final: 0.7509 (t80) REVERT: B 352 LEU cc_start: 0.8259 (tt) cc_final: 0.8024 (mp) REVERT: B 538 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8148 (mtp85) REVERT: B 564 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 715 GLU cc_start: 0.5886 (mm-30) cc_final: 0.4188 (mp0) REVERT: B 828 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.8012 (ttp80) REVERT: B 930 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6629 (tpt) REVERT: B 1011 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8631 (ttmm) REVERT: B 1204 LEU cc_start: 0.8302 (mt) cc_final: 0.8099 (mp) outliers start: 84 outliers final: 46 residues processed: 392 average time/residue: 1.1839 time to fit residues: 566.7466 Evaluate side-chains 380 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 3.322 ------------------------------------------------------------------------------- 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 231 LEU 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 716 LEU Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 385 LEU 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 627 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 981 GLN 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 280 CYS Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 828 ARG Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 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 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 7 optimal weight: 8.9990 chunk 211 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 180 optimal weight: 40.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 GLN D1159 HIS A 981 GLN A1159 HIS C 218 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.102479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079951 restraints weight = 73453.356| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.84 r_work: 0.3143 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29356 Z= 0.198 Angle : 0.703 13.580 39896 Z= 0.333 Chirality : 0.047 0.924 4556 Planarity : 0.004 0.061 5008 Dihedral : 5.552 51.974 3984 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.43 % Allowed : 28.79 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3552 helix: 1.09 (0.13), residues: 1712 sheet: -0.37 (0.28), residues: 344 loop : 0.38 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 325 HIS 0.041 0.002 HIS B 291 PHE 0.034 0.002 PHE D 305 TYR 0.022 0.002 TYR A1167 ARG 0.012 0.001 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1376) hydrogen bonds : angle 4.19791 ( 3876) metal coordination : bond 0.00755 ( 16) metal coordination : angle 1.25959 ( 12) covalent geometry : bond 0.00484 (29340) covalent geometry : angle 0.70233 (39884) ********************** 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 418 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 PHE cc_start: 0.8212 (t80) cc_final: 0.7639 (m-80) REVERT: D 192 MET cc_start: 0.7627 (mmm) cc_final: 0.7148 (mmm) REVERT: D 216 MET cc_start: 0.7275 (tpp) cc_final: 0.6961 (tpp) REVERT: D 274 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8790 (tp) REVERT: D 548 GLN cc_start: 0.7727 (tp40) cc_final: 0.7518 (tp40) REVERT: D 715 GLU cc_start: 0.7404 (mp0) cc_final: 0.7130 (mp0) REVERT: D 844 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: D 936 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: D 948 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7751 (ptp-110) REVERT: D 1017 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8394 (mm) REVERT: A 163 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7785 (p0) REVERT: A 192 MET cc_start: 0.7511 (mpm) cc_final: 0.7042 (mpt) REVERT: A 216 MET cc_start: 0.8171 (mtm) cc_final: 0.7458 (tpt) REVERT: A 231 LEU cc_start: 0.8133 (mm) cc_final: 0.7842 (tp) REVERT: A 354 MET cc_start: 0.8457 (mmm) cc_final: 0.8243 (mmt) REVERT: A 356 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7909 (ppp80) REVERT: A 447 MET cc_start: 0.8699 (mmm) cc_final: 0.8420 (tpt) REVERT: A 473 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 799 LYS cc_start: 0.8741 (pttp) cc_final: 0.8384 (ptmm) REVERT: A 972 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7355 (mm) REVERT: C 216 MET cc_start: 0.8201 (mmt) cc_final: 0.7768 (mmm) REVERT: C 268 PHE cc_start: 0.8347 (t80) cc_final: 0.8084 (t80) REVERT: C 276 CYS cc_start: 0.8593 (m) cc_final: 0.8294 (p) REVERT: C 279 LEU cc_start: 0.8804 (tm) cc_final: 0.8565 (tt) REVERT: C 447 MET cc_start: 0.8386 (mmm) cc_final: 0.7885 (tpp) REVERT: C 773 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8364 (ptmt) REVERT: C 829 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8252 (mttp) REVERT: C 930 MET cc_start: 0.7453 (tpt) cc_final: 0.6805 (tpt) REVERT: B 204 TRP cc_start: 0.5605 (t-100) cc_final: 0.5292 (t60) REVERT: B 216 MET cc_start: 0.8116 (ttp) cc_final: 0.7640 (tpp) REVERT: B 222 PHE cc_start: 0.8259 (m-80) cc_final: 0.7594 (t80) REVERT: B 564 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8071 (tp) REVERT: B 712 PRO cc_start: 0.8188 (Cg_exo) cc_final: 0.7931 (Cg_endo) REVERT: B 715 GLU cc_start: 0.6148 (mm-30) cc_final: 0.4547 (mp0) REVERT: B 930 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6842 (tpt) REVERT: B 1011 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8723 (ttmm) REVERT: B 1204 LEU cc_start: 0.8286 (mt) cc_final: 0.8034 (mp) outliers start: 75 outliers final: 39 residues processed: 398 average time/residue: 1.1236 time to fit residues: 541.6427 Evaluate side-chains 378 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 328 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 844 HIS 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 D residue 1162 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 356 ARG 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 627 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 972 ILE 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 280 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 930 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 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 66 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 258 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 322 optimal weight: 0.0010 chunk 328 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS ** A 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS C 291 HIS C1159 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.104034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080906 restraints weight = 72930.995| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.85 r_work: 0.3177 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.8158 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= 0.138 Angle : 0.685 13.219 39896 Z= 0.322 Chirality : 0.043 0.314 4556 Planarity : 0.004 0.066 5008 Dihedral : 5.446 51.470 3984 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.20 % Allowed : 29.08 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3552 helix: 1.13 (0.13), residues: 1728 sheet: -0.42 (0.28), residues: 344 loop : 0.36 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 325 HIS 0.044 0.002 HIS B 291 PHE 0.036 0.002 PHE A 235 TYR 0.046 0.001 TYR B 317 ARG 0.010 0.000 ARG B 418 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 1376) hydrogen bonds : angle 4.13813 ( 3876) metal coordination : bond 0.00511 ( 16) metal coordination : angle 1.19624 ( 12) covalent geometry : bond 0.00327 (29340) covalent geometry : angle 0.68453 (39884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19961.74 seconds wall clock time: 351 minutes 21.99 seconds (21081.99 seconds total)