Starting phenix.real_space_refine on Sun Nov 17 06:24:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/11_2024/8f1d_28795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/11_2024/8f1d_28795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/11_2024/8f1d_28795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/11_2024/8f1d_28795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/11_2024/8f1d_28795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1d_28795/11_2024/8f1d_28795.cif" } resolution = 2.94 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= 0.012 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 S 68 5.16 5 C 8484 2.51 5 N 2152 2.21 5 O 2176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3192 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Unusual residues: {' K': 4, ' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' ZN': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 800 SG CYS A 104 66.035 80.119 76.719 1.00193.00 S ATOM 806 SG CYS A 105 62.642 78.693 77.855 1.00202.39 S ATOM 3823 SG CYS B 83 65.774 76.456 77.997 1.00207.60 S ATOM 3992 SG CYS B 104 80.119 65.001 76.713 1.00193.69 S ATOM 3998 SG CYS B 105 78.699 68.394 77.855 1.00202.98 S ATOM 7015 SG CYS C 83 76.457 65.265 77.996 1.00206.73 S ATOM 7184 SG CYS C 104 65.002 50.920 76.716 1.00193.64 S ATOM 7190 SG CYS C 105 68.394 52.343 77.858 1.00202.41 S ATOM 10207 SG CYS D 83 65.264 54.584 77.994 1.00206.45 S ATOM 631 SG CYS A 83 54.583 65.775 77.995 1.00206.51 S ATOM 10376 SG CYS D 104 50.921 66.039 76.712 1.00194.05 S ATOM 10382 SG CYS D 105 52.340 62.646 77.854 1.00201.59 S Time building chain proxies: 8.23, per 1000 atoms: 0.64 Number of scatterers: 12888 At special positions: 0 Unit cell: (131.88, 131.88, 124.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 K 4 19.00 S 68 16.00 O 2176 8.00 N 2152 7.00 C 8484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 601 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 104 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 601 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 104 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " Number of angles added : 12 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 68.5% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.811A pdb=" N ILE A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.748A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.587A pdb=" N TRP A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.816A pdb=" N ALA A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.505A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 210 removed outlier: 3.764A pdb=" N TYR A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 3.964A pdb=" N GLU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 276 through 295 removed outlier: 3.688A pdb=" N ILE A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 320 through 325 removed outlier: 4.238A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 Processing helix chain 'A' and resid 341 through 367 removed outlier: 3.602A pdb=" N PHE A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 removed outlier: 4.005A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.920A pdb=" N LEU A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.675A pdb=" N LYS A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.811A pdb=" N ILE B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.531A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.588A pdb=" N TRP B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.818A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 187 through 210 removed outlier: 3.753A pdb=" N TYR B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.969A pdb=" N GLU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 276 through 295 removed outlier: 3.689A pdb=" N ILE B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Proline residue: B 288 - end of helix Processing helix chain 'B' and resid 299 through 314 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.218A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 341 through 367 removed outlier: 3.603A pdb=" N PHE B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.005A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.924A pdb=" N LEU B 415 " --> pdb=" O TRP B 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.683A pdb=" N LYS B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.810A pdb=" N ILE C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.509A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.587A pdb=" N TRP C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.820A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.504A pdb=" N PHE C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 210 removed outlier: 3.771A pdb=" N TYR C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 266 removed outlier: 4.005A pdb=" N GLU C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.689A pdb=" N ILE C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 299 through 314 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 320 through 325 removed outlier: 4.236A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 Processing helix chain 'C' and resid 341 through 367 removed outlier: 3.597A pdb=" N PHE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 399 removed outlier: 4.005A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 removed outlier: 3.915A pdb=" N LEU C 415 " --> pdb=" O TRP C 411 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.672A pdb=" N LYS C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.812A pdb=" N ILE D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.531A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.588A pdb=" N TRP D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.817A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.501A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 210 removed outlier: 3.761A pdb=" N TYR D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 266 removed outlier: 3.963A pdb=" N GLU D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 276 through 295 removed outlier: 3.689A pdb=" N ILE D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) Proline residue: D 288 - end of helix Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 320 through 325 removed outlier: 4.237A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 341 through 367 removed outlier: 3.598A pdb=" N PHE D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 399 removed outlier: 4.006A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 removed outlier: 3.924A pdb=" N LEU D 415 " --> pdb=" O TRP D 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.635A pdb=" N LYS D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.951A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 49 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.514A pdb=" N PHE B 55 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 49 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.517A pdb=" N PHE C 55 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP C 49 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.515A pdb=" N PHE D 55 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D 49 " --> pdb=" O GLU D 54 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 2010 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: 3.52 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3978 1.34 - 1.46: 2748 1.46 - 1.57: 6446 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 13276 Sorted by residual: bond pdb=" C MET B 430 " pdb=" N PRO B 431 " ideal model delta sigma weight residual 1.336 1.366 -0.031 9.80e-03 1.04e+04 9.70e+00 bond pdb=" C MET C 430 " pdb=" N PRO C 431 " ideal model delta sigma weight residual 1.336 1.366 -0.031 9.80e-03 1.04e+04 9.70e+00 bond pdb=" C MET A 430 " pdb=" N PRO A 431 " ideal model delta sigma weight residual 1.336 1.366 -0.030 9.80e-03 1.04e+04 9.53e+00 bond pdb=" C MET D 430 " pdb=" N PRO D 431 " ideal model delta sigma weight residual 1.336 1.366 -0.030 9.80e-03 1.04e+04 9.45e+00 bond pdb=" N LYS A 457 " pdb=" CA LYS A 457 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.17e-01 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 17575 1.25 - 2.50: 372 2.50 - 3.75: 95 3.75 - 5.01: 18 5.01 - 6.26: 12 Bond angle restraints: 18072 Sorted by residual: angle pdb=" CA PRO D 431 " pdb=" C PRO D 431 " pdb=" O PRO D 431 " ideal model delta sigma weight residual 118.78 121.55 -2.77 1.40e+00 5.10e-01 3.92e+00 angle pdb=" CA PRO C 431 " pdb=" C PRO C 431 " pdb=" O PRO C 431 " ideal model delta sigma weight residual 118.78 121.54 -2.76 1.40e+00 5.10e-01 3.88e+00 angle pdb=" CA PRO A 431 " pdb=" C PRO A 431 " pdb=" O PRO A 431 " ideal model delta sigma weight residual 118.78 121.54 -2.76 1.40e+00 5.10e-01 3.88e+00 angle pdb=" CA PRO B 431 " pdb=" C PRO B 431 " pdb=" O PRO B 431 " ideal model delta sigma weight residual 118.78 121.50 -2.72 1.40e+00 5.10e-01 3.77e+00 angle pdb=" N LEU B 287 " pdb=" CA LEU B 287 " pdb=" C LEU B 287 " ideal model delta sigma weight residual 112.75 115.33 -2.58 1.36e+00 5.41e-01 3.60e+00 ... (remaining 18067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 7392 16.27 - 32.53: 431 32.53 - 48.80: 73 48.80 - 65.07: 8 65.07 - 81.33: 4 Dihedral angle restraints: 7908 sinusoidal: 3300 harmonic: 4608 Sorted by residual: dihedral pdb=" N LEU C 245 " pdb=" CA LEU C 245 " pdb=" CB LEU C 245 " pdb=" CG LEU C 245 " ideal model delta sinusoidal sigma weight residual -60.00 -118.99 58.99 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU D 245 " pdb=" CA LEU D 245 " pdb=" CB LEU D 245 " pdb=" CG LEU D 245 " ideal model delta sinusoidal sigma weight residual -60.00 -118.15 58.15 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 245 " pdb=" CA LEU A 245 " pdb=" CB LEU A 245 " pdb=" CG LEU A 245 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 7905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1136 0.028 - 0.056: 583 0.056 - 0.085: 174 0.085 - 0.113: 76 0.113 - 0.141: 23 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CA MET B 430 " pdb=" N MET B 430 " pdb=" C MET B 430 " pdb=" CB MET B 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA MET A 430 " pdb=" N MET A 430 " pdb=" C MET A 430 " pdb=" CB MET A 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA MET C 430 " pdb=" N MET C 430 " pdb=" C MET C 430 " pdb=" CB MET C 430 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1989 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 84 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO D 85 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 84 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 85 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 84 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 85 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.024 5.00e-02 4.00e+02 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.89: 4861 2.89 - 3.45: 14916 3.45 - 4.01: 22112 4.01 - 4.58: 32522 4.58 - 5.14: 45463 Nonbonded interactions: 119874 Sorted by model distance: nonbonded pdb=" NH1 ARG C 33 " pdb=" O PHE C 93 " model vdw 2.321 3.120 nonbonded pdb=" NH1 ARG A 33 " pdb=" O PHE A 93 " model vdw 2.322 3.120 nonbonded pdb=" NH1 ARG D 33 " pdb=" O PHE D 93 " model vdw 2.322 3.120 nonbonded pdb=" NH1 ARG B 33 " pdb=" O PHE B 93 " model vdw 2.323 3.120 nonbonded pdb=" O THR D 399 " pdb=" OG1 THR D 400 " model vdw 2.416 3.040 ... (remaining 119869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 463 or resid 601 through 602)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.240 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13276 Z= 0.277 Angle : 0.509 6.258 18072 Z= 0.259 Chirality : 0.039 0.141 1992 Planarity : 0.004 0.043 2244 Dihedral : 10.401 81.332 4932 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.59 % Allowed : 5.04 % Favored : 94.36 % 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: 1.12 (0.22), residues: 1552 helix: 1.63 (0.17), residues: 948 sheet: 1.46 (0.82), residues: 40 loop : -0.84 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 392 HIS 0.002 0.001 HIS C 66 PHE 0.007 0.001 PHE D 244 TYR 0.008 0.001 TYR B 365 ARG 0.002 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 1.457 Fit side-chains REVERT: A 182 ASP cc_start: 0.7001 (t0) cc_final: 0.6703 (t0) REVERT: A 213 GLU cc_start: 0.5954 (mp0) cc_final: 0.5674 (mp0) REVERT: A 275 LYS cc_start: 0.7147 (mttt) cc_final: 0.6472 (tptt) REVERT: A 295 LEU cc_start: 0.6683 (tp) cc_final: 0.6439 (tt) REVERT: A 339 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6609 (ttm110) REVERT: A 437 ASN cc_start: 0.6283 (t0) cc_final: 0.5941 (m-40) REVERT: A 451 LYS cc_start: 0.6797 (mmpt) cc_final: 0.6411 (mttt) REVERT: A 457 LYS cc_start: 0.6164 (pttt) cc_final: 0.5791 (tptm) REVERT: A 458 LYS cc_start: 0.6502 (mmmt) cc_final: 0.6220 (mtmt) REVERT: B 182 ASP cc_start: 0.7006 (t0) cc_final: 0.6709 (t0) REVERT: B 213 GLU cc_start: 0.5885 (mp0) cc_final: 0.5565 (mp0) REVERT: B 275 LYS cc_start: 0.7156 (mttt) cc_final: 0.6481 (tptt) REVERT: B 295 LEU cc_start: 0.6713 (tp) cc_final: 0.6453 (tt) REVERT: B 339 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6597 (ttm110) REVERT: B 437 ASN cc_start: 0.6269 (t0) cc_final: 0.5928 (m-40) REVERT: B 451 LYS cc_start: 0.6707 (mmpt) cc_final: 0.6316 (mttt) REVERT: B 458 LYS cc_start: 0.6551 (mmmt) cc_final: 0.6178 (ttpt) REVERT: C 182 ASP cc_start: 0.7000 (t0) cc_final: 0.6703 (t0) REVERT: C 213 GLU cc_start: 0.5875 (mp0) cc_final: 0.5562 (mp0) REVERT: C 275 LYS cc_start: 0.7116 (mttt) cc_final: 0.6396 (tptt) REVERT: C 295 LEU cc_start: 0.6699 (tp) cc_final: 0.6444 (tt) REVERT: C 339 ARG cc_start: 0.6763 (ttp-170) cc_final: 0.6559 (ttm110) REVERT: C 437 ASN cc_start: 0.6287 (t0) cc_final: 0.5947 (m-40) REVERT: C 451 LYS cc_start: 0.6786 (mmpt) cc_final: 0.6401 (mttt) REVERT: C 457 LYS cc_start: 0.6187 (pttt) cc_final: 0.5814 (tmtt) REVERT: C 458 LYS cc_start: 0.6533 (mmmt) cc_final: 0.6241 (mtmt) REVERT: D 182 ASP cc_start: 0.7004 (t0) cc_final: 0.6707 (t0) REVERT: D 213 GLU cc_start: 0.5960 (mp0) cc_final: 0.5677 (mp0) REVERT: D 275 LYS cc_start: 0.7144 (mttt) cc_final: 0.6471 (tptt) REVERT: D 295 LEU cc_start: 0.6693 (tp) cc_final: 0.6428 (tt) REVERT: D 339 ARG cc_start: 0.6771 (ttp-170) cc_final: 0.6568 (ttm110) REVERT: D 437 ASN cc_start: 0.6314 (t0) cc_final: 0.5970 (m-40) REVERT: D 451 LYS cc_start: 0.6793 (mmpt) cc_final: 0.6404 (mttt) REVERT: D 457 LYS cc_start: 0.6301 (pttt) cc_final: 0.5892 (tptm) REVERT: D 458 LYS cc_start: 0.6463 (mmmt) cc_final: 0.6252 (mtpt) outliers start: 8 outliers final: 0 residues processed: 231 average time/residue: 1.1984 time to fit residues: 302.9996 Evaluate side-chains 159 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 43 HIS C 43 HIS D 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13276 Z= 0.408 Angle : 0.669 9.579 18072 Z= 0.334 Chirality : 0.047 0.146 1992 Planarity : 0.005 0.047 2244 Dihedral : 5.051 38.269 1996 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.78 % Allowed : 10.24 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.22), residues: 1552 helix: 1.20 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -0.86 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 392 HIS 0.004 0.001 HIS A 383 PHE 0.017 0.002 PHE D 56 TYR 0.014 0.002 TYR D 365 ARG 0.006 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.491 Fit side-chains REVERT: A 182 ASP cc_start: 0.6688 (t70) cc_final: 0.6333 (t0) REVERT: A 275 LYS cc_start: 0.7088 (mttt) cc_final: 0.6497 (tptt) REVERT: A 295 LEU cc_start: 0.6709 (tp) cc_final: 0.6410 (tt) REVERT: A 318 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6993 (mm) REVERT: A 437 ASN cc_start: 0.6376 (t0) cc_final: 0.5990 (m-40) REVERT: A 451 LYS cc_start: 0.6758 (mmpt) cc_final: 0.6379 (mttt) REVERT: A 457 LYS cc_start: 0.6164 (pttt) cc_final: 0.5812 (tmtt) REVERT: A 458 LYS cc_start: 0.6388 (mmmt) cc_final: 0.6188 (mtmt) REVERT: B 182 ASP cc_start: 0.6583 (t70) cc_final: 0.6220 (t0) REVERT: B 275 LYS cc_start: 0.7096 (mttt) cc_final: 0.6508 (tptt) REVERT: B 295 LEU cc_start: 0.6715 (tp) cc_final: 0.6393 (tt) REVERT: B 318 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6996 (mm) REVERT: B 437 ASN cc_start: 0.6363 (t0) cc_final: 0.5979 (m-40) REVERT: B 451 LYS cc_start: 0.6785 (mmpt) cc_final: 0.6390 (mttt) REVERT: B 458 LYS cc_start: 0.6474 (mmmt) cc_final: 0.6155 (ttmt) REVERT: C 98 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: C 182 ASP cc_start: 0.6684 (t70) cc_final: 0.6330 (t0) REVERT: C 275 LYS cc_start: 0.7118 (mttt) cc_final: 0.6472 (tptt) REVERT: C 295 LEU cc_start: 0.6683 (tp) cc_final: 0.6360 (tt) REVERT: C 318 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.7005 (mm) REVERT: C 437 ASN cc_start: 0.6382 (t0) cc_final: 0.5997 (m-40) REVERT: C 451 LYS cc_start: 0.6730 (mmpt) cc_final: 0.6408 (mttt) REVERT: C 457 LYS cc_start: 0.6182 (pttt) cc_final: 0.5827 (tmtt) REVERT: C 458 LYS cc_start: 0.6395 (mmmt) cc_final: 0.6189 (mtmt) REVERT: D 98 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: D 182 ASP cc_start: 0.6691 (t70) cc_final: 0.6337 (t0) REVERT: D 275 LYS cc_start: 0.7089 (mttt) cc_final: 0.6498 (tptt) REVERT: D 295 LEU cc_start: 0.6707 (tp) cc_final: 0.6386 (tt) REVERT: D 318 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.7006 (mm) REVERT: D 437 ASN cc_start: 0.6345 (t0) cc_final: 0.5961 (m-40) REVERT: D 451 LYS cc_start: 0.6691 (mmpt) cc_final: 0.6324 (mttt) REVERT: D 457 LYS cc_start: 0.6165 (pttt) cc_final: 0.5845 (tmtt) outliers start: 24 outliers final: 12 residues processed: 180 average time/residue: 1.0826 time to fit residues: 216.3237 Evaluate side-chains 185 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 406 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13276 Z= 0.269 Angle : 0.570 7.015 18072 Z= 0.288 Chirality : 0.042 0.129 1992 Planarity : 0.005 0.047 2244 Dihedral : 5.087 46.019 1996 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.26 % Allowed : 11.05 % Favored : 87.69 % 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: 0.58 (0.22), residues: 1552 helix: 1.20 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -0.94 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.002 0.001 HIS D 60 PHE 0.024 0.002 PHE B 56 TYR 0.009 0.001 TYR B 365 ARG 0.002 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.560 Fit side-chains REVERT: A 56 PHE cc_start: 0.7605 (t80) cc_final: 0.7006 (t80) REVERT: A 182 ASP cc_start: 0.6604 (t70) cc_final: 0.6158 (t70) REVERT: A 275 LYS cc_start: 0.7112 (mttt) cc_final: 0.6431 (tptt) REVERT: A 295 LEU cc_start: 0.6711 (tp) cc_final: 0.6429 (tt) REVERT: A 414 MET cc_start: 0.6451 (mtt) cc_final: 0.6232 (mtt) REVERT: A 437 ASN cc_start: 0.6344 (t0) cc_final: 0.5948 (m110) REVERT: A 451 LYS cc_start: 0.6763 (mmpt) cc_final: 0.6429 (mttt) REVERT: A 457 LYS cc_start: 0.6144 (pttt) cc_final: 0.5776 (tmtt) REVERT: B 182 ASP cc_start: 0.6549 (t70) cc_final: 0.6135 (t70) REVERT: B 275 LYS cc_start: 0.7123 (mttt) cc_final: 0.6430 (tptt) REVERT: B 295 LEU cc_start: 0.6727 (tp) cc_final: 0.6423 (tt) REVERT: B 414 MET cc_start: 0.6470 (mtt) cc_final: 0.6247 (mtt) REVERT: B 437 ASN cc_start: 0.6331 (t0) cc_final: 0.5937 (m110) REVERT: B 451 LYS cc_start: 0.6798 (mmpt) cc_final: 0.6410 (mttt) REVERT: B 458 LYS cc_start: 0.6376 (mmmt) cc_final: 0.6079 (mtmt) REVERT: C 182 ASP cc_start: 0.6599 (t70) cc_final: 0.6154 (t70) REVERT: C 275 LYS cc_start: 0.7123 (mttt) cc_final: 0.6438 (tptt) REVERT: C 295 LEU cc_start: 0.6770 (tp) cc_final: 0.6467 (tt) REVERT: C 437 ASN cc_start: 0.6348 (t0) cc_final: 0.5953 (m110) REVERT: C 451 LYS cc_start: 0.6738 (mmpt) cc_final: 0.6414 (mttt) REVERT: C 457 LYS cc_start: 0.6160 (pttt) cc_final: 0.5788 (tmtt) REVERT: D 182 ASP cc_start: 0.6610 (t70) cc_final: 0.6164 (t70) REVERT: D 275 LYS cc_start: 0.7114 (mttt) cc_final: 0.6434 (tptt) REVERT: D 295 LEU cc_start: 0.6738 (tp) cc_final: 0.6464 (tt) REVERT: D 414 MET cc_start: 0.6451 (mtt) cc_final: 0.6230 (mtt) REVERT: D 437 ASN cc_start: 0.6349 (t0) cc_final: 0.5957 (m110) REVERT: D 451 LYS cc_start: 0.6773 (mmpt) cc_final: 0.6403 (mttt) REVERT: D 457 LYS cc_start: 0.6170 (pttt) cc_final: 0.5825 (tmtt) outliers start: 17 outliers final: 11 residues processed: 183 average time/residue: 0.9912 time to fit residues: 202.7529 Evaluate side-chains 181 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 406 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13276 Z= 0.258 Angle : 0.571 8.878 18072 Z= 0.286 Chirality : 0.041 0.131 1992 Planarity : 0.005 0.049 2244 Dihedral : 5.237 49.552 1996 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.93 % Allowed : 12.61 % Favored : 85.46 % 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: 0.53 (0.22), residues: 1552 helix: 1.19 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -1.02 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.002 0.001 HIS A 60 PHE 0.026 0.002 PHE B 56 TYR 0.009 0.001 TYR C 365 ARG 0.002 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.499 Fit side-chains REVERT: A 182 ASP cc_start: 0.6572 (t70) cc_final: 0.6107 (t70) REVERT: A 275 LYS cc_start: 0.7163 (mttt) cc_final: 0.6442 (tptt) REVERT: A 295 LEU cc_start: 0.6790 (tp) cc_final: 0.6502 (tt) REVERT: A 318 ILE cc_start: 0.7081 (tt) cc_final: 0.6850 (mm) REVERT: A 437 ASN cc_start: 0.6356 (t0) cc_final: 0.5936 (m-40) REVERT: A 451 LYS cc_start: 0.6760 (mmpt) cc_final: 0.6432 (mttt) REVERT: A 457 LYS cc_start: 0.6113 (pttt) cc_final: 0.5751 (tmtt) REVERT: B 182 ASP cc_start: 0.6533 (t70) cc_final: 0.6093 (t70) REVERT: B 269 ASN cc_start: 0.7707 (t0) cc_final: 0.7490 (t0) REVERT: B 275 LYS cc_start: 0.7152 (mttt) cc_final: 0.6371 (tptp) REVERT: B 295 LEU cc_start: 0.6822 (tp) cc_final: 0.6531 (tt) REVERT: B 437 ASN cc_start: 0.6344 (t0) cc_final: 0.5924 (m-40) REVERT: B 451 LYS cc_start: 0.6760 (mmpt) cc_final: 0.6429 (mttt) REVERT: B 458 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6058 (mtmt) REVERT: C 182 ASP cc_start: 0.6568 (t70) cc_final: 0.6104 (t70) REVERT: C 275 LYS cc_start: 0.7162 (mttt) cc_final: 0.6344 (tptp) REVERT: C 295 LEU cc_start: 0.6791 (tp) cc_final: 0.6493 (tt) REVERT: C 437 ASN cc_start: 0.6363 (t0) cc_final: 0.5941 (m-40) REVERT: C 451 LYS cc_start: 0.6758 (mmpt) cc_final: 0.6433 (mttt) REVERT: C 457 LYS cc_start: 0.6099 (pttt) cc_final: 0.5731 (tmtt) REVERT: D 182 ASP cc_start: 0.6576 (t70) cc_final: 0.6112 (t70) REVERT: D 269 ASN cc_start: 0.7681 (t0) cc_final: 0.7472 (t0) REVERT: D 275 LYS cc_start: 0.7166 (mttt) cc_final: 0.6444 (tptt) REVERT: D 295 LEU cc_start: 0.6810 (tp) cc_final: 0.6521 (tt) REVERT: D 318 ILE cc_start: 0.7082 (tt) cc_final: 0.6843 (mm) REVERT: D 437 ASN cc_start: 0.6327 (t0) cc_final: 0.5935 (m-40) REVERT: D 451 LYS cc_start: 0.6751 (mmpt) cc_final: 0.6421 (mttt) REVERT: D 457 LYS cc_start: 0.6183 (pttt) cc_final: 0.5826 (tmtt) outliers start: 26 outliers final: 19 residues processed: 191 average time/residue: 0.9581 time to fit residues: 204.7527 Evaluate side-chains 188 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 0.3980 chunk 62 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13276 Z= 0.208 Angle : 0.523 7.441 18072 Z= 0.264 Chirality : 0.040 0.128 1992 Planarity : 0.004 0.047 2244 Dihedral : 5.170 54.027 1996 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.56 % Allowed : 13.06 % Favored : 85.39 % 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: 0.65 (0.22), residues: 1552 helix: 1.30 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -0.99 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS A 60 PHE 0.021 0.001 PHE A 56 TYR 0.007 0.001 TYR B 48 ARG 0.001 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.461 Fit side-chains REVERT: A 182 ASP cc_start: 0.6584 (t70) cc_final: 0.6127 (t70) REVERT: A 275 LYS cc_start: 0.7212 (mttt) cc_final: 0.6423 (tptp) REVERT: A 295 LEU cc_start: 0.6840 (tp) cc_final: 0.6565 (tt) REVERT: A 318 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6864 (mm) REVERT: A 437 ASN cc_start: 0.6355 (t0) cc_final: 0.5981 (m110) REVERT: A 451 LYS cc_start: 0.6742 (mmpt) cc_final: 0.6427 (mttt) REVERT: A 457 LYS cc_start: 0.6135 (pttt) cc_final: 0.5781 (tmtt) REVERT: B 182 ASP cc_start: 0.6569 (t70) cc_final: 0.6155 (t70) REVERT: B 275 LYS cc_start: 0.7223 (mttt) cc_final: 0.6416 (tptp) REVERT: B 295 LEU cc_start: 0.6869 (tp) cc_final: 0.6606 (tt) REVERT: B 437 ASN cc_start: 0.6341 (t0) cc_final: 0.5969 (m110) REVERT: B 451 LYS cc_start: 0.6760 (mmpt) cc_final: 0.6432 (mttt) REVERT: B 458 LYS cc_start: 0.6401 (mmmt) cc_final: 0.6148 (mtmt) REVERT: C 182 ASP cc_start: 0.6583 (t70) cc_final: 0.6127 (t70) REVERT: C 275 LYS cc_start: 0.7210 (mttt) cc_final: 0.6392 (tptp) REVERT: C 295 LEU cc_start: 0.6706 (tp) cc_final: 0.6444 (tt) REVERT: C 437 ASN cc_start: 0.6360 (t0) cc_final: 0.5986 (m110) REVERT: C 451 LYS cc_start: 0.6726 (mmpt) cc_final: 0.6416 (mttt) REVERT: C 457 LYS cc_start: 0.5971 (pttt) cc_final: 0.5649 (tmtt) REVERT: D 182 ASP cc_start: 0.6582 (t70) cc_final: 0.6124 (t70) REVERT: D 275 LYS cc_start: 0.7220 (mttt) cc_final: 0.6480 (tptt) REVERT: D 295 LEU cc_start: 0.6813 (tp) cc_final: 0.6534 (tt) REVERT: D 318 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6857 (mm) REVERT: D 437 ASN cc_start: 0.6382 (t0) cc_final: 0.6007 (m110) REVERT: D 451 LYS cc_start: 0.6755 (mmpt) cc_final: 0.6430 (mttt) outliers start: 21 outliers final: 14 residues processed: 184 average time/residue: 1.0332 time to fit residues: 212.3204 Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13276 Z= 0.204 Angle : 0.530 9.890 18072 Z= 0.266 Chirality : 0.040 0.128 1992 Planarity : 0.004 0.048 2244 Dihedral : 5.187 57.811 1996 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.85 % Allowed : 13.28 % Favored : 84.87 % 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: 0.66 (0.22), residues: 1552 helix: 1.30 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -0.99 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS B 60 PHE 0.020 0.001 PHE B 56 TYR 0.007 0.001 TYR B 48 ARG 0.001 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.407 Fit side-chains REVERT: A 182 ASP cc_start: 0.6589 (t70) cc_final: 0.6128 (t70) REVERT: A 265 ILE cc_start: 0.7073 (mt) cc_final: 0.6730 (pt) REVERT: A 275 LYS cc_start: 0.7229 (mttt) cc_final: 0.6439 (tptp) REVERT: A 295 LEU cc_start: 0.6765 (tp) cc_final: 0.6528 (tt) REVERT: A 318 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6848 (mm) REVERT: A 437 ASN cc_start: 0.6386 (t0) cc_final: 0.5999 (m110) REVERT: A 451 LYS cc_start: 0.6753 (mmpt) cc_final: 0.6427 (mttt) REVERT: A 457 LYS cc_start: 0.6135 (pttt) cc_final: 0.5773 (tmtt) REVERT: B 182 ASP cc_start: 0.6578 (t70) cc_final: 0.6164 (t70) REVERT: B 265 ILE cc_start: 0.7190 (mt) cc_final: 0.6845 (pt) REVERT: B 275 LYS cc_start: 0.7248 (mttt) cc_final: 0.6415 (tptp) REVERT: B 295 LEU cc_start: 0.6788 (tp) cc_final: 0.6544 (tt) REVERT: B 437 ASN cc_start: 0.6371 (t0) cc_final: 0.5987 (m110) REVERT: B 451 LYS cc_start: 0.6757 (mmpt) cc_final: 0.6429 (mttt) REVERT: B 458 LYS cc_start: 0.6406 (mmmt) cc_final: 0.6159 (mtmt) REVERT: C 182 ASP cc_start: 0.6593 (t70) cc_final: 0.6126 (t70) REVERT: C 275 LYS cc_start: 0.7254 (mttt) cc_final: 0.6420 (tptp) REVERT: C 295 LEU cc_start: 0.6742 (tp) cc_final: 0.6483 (tt) REVERT: C 437 ASN cc_start: 0.6388 (t0) cc_final: 0.6003 (m110) REVERT: C 451 LYS cc_start: 0.6724 (mmpt) cc_final: 0.6413 (mttt) REVERT: D 182 ASP cc_start: 0.6594 (t70) cc_final: 0.6136 (t70) REVERT: D 265 ILE cc_start: 0.7202 (mt) cc_final: 0.6881 (pt) REVERT: D 275 LYS cc_start: 0.7211 (mttt) cc_final: 0.6426 (tptp) REVERT: D 295 LEU cc_start: 0.6789 (tp) cc_final: 0.6548 (tt) REVERT: D 318 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6880 (mm) REVERT: D 437 ASN cc_start: 0.6390 (t0) cc_final: 0.6006 (m110) REVERT: D 451 LYS cc_start: 0.6752 (mmpt) cc_final: 0.6427 (mttt) outliers start: 25 outliers final: 19 residues processed: 187 average time/residue: 0.9676 time to fit residues: 202.3685 Evaluate side-chains 186 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.2980 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 94 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13276 Z= 0.146 Angle : 0.475 7.615 18072 Z= 0.242 Chirality : 0.038 0.130 1992 Planarity : 0.004 0.045 2244 Dihedral : 4.958 57.640 1996 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.08 % Allowed : 13.20 % Favored : 84.72 % 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: 0.94 (0.22), residues: 1552 helix: 1.50 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 411 HIS 0.001 0.000 HIS A 60 PHE 0.017 0.001 PHE A 56 TYR 0.007 0.001 TYR B 48 ARG 0.002 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.396 Fit side-chains REVERT: A 32 THR cc_start: 0.3750 (OUTLIER) cc_final: 0.3522 (p) REVERT: A 182 ASP cc_start: 0.6584 (t70) cc_final: 0.6119 (t70) REVERT: A 265 ILE cc_start: 0.7132 (mt) cc_final: 0.6797 (pt) REVERT: A 275 LYS cc_start: 0.7184 (mttt) cc_final: 0.6411 (tptp) REVERT: A 437 ASN cc_start: 0.6336 (t0) cc_final: 0.5939 (m110) REVERT: A 451 LYS cc_start: 0.6772 (mmpt) cc_final: 0.6445 (mttt) REVERT: A 457 LYS cc_start: 0.6033 (pttt) cc_final: 0.5692 (tmtt) REVERT: B 32 THR cc_start: 0.3921 (OUTLIER) cc_final: 0.3693 (p) REVERT: B 182 ASP cc_start: 0.6565 (t70) cc_final: 0.6148 (t70) REVERT: B 265 ILE cc_start: 0.7171 (mt) cc_final: 0.6846 (pt) REVERT: B 275 LYS cc_start: 0.7243 (mttt) cc_final: 0.6458 (tptp) REVERT: B 437 ASN cc_start: 0.6338 (t0) cc_final: 0.5937 (m110) REVERT: B 451 LYS cc_start: 0.6758 (mmpt) cc_final: 0.6433 (mttt) REVERT: B 458 LYS cc_start: 0.6383 (mmmt) cc_final: 0.6136 (mtmt) REVERT: C 32 THR cc_start: 0.3896 (OUTLIER) cc_final: 0.3670 (p) REVERT: C 182 ASP cc_start: 0.6549 (t70) cc_final: 0.6097 (t70) REVERT: C 265 ILE cc_start: 0.7138 (mt) cc_final: 0.6868 (pt) REVERT: C 275 LYS cc_start: 0.7231 (mttt) cc_final: 0.6447 (tptp) REVERT: C 437 ASN cc_start: 0.6338 (t0) cc_final: 0.5937 (m110) REVERT: C 451 LYS cc_start: 0.6754 (mmpt) cc_final: 0.6427 (mttt) REVERT: D 32 THR cc_start: 0.3912 (OUTLIER) cc_final: 0.3684 (p) REVERT: D 182 ASP cc_start: 0.6625 (t70) cc_final: 0.6160 (t70) REVERT: D 265 ILE cc_start: 0.7167 (mt) cc_final: 0.6855 (pt) REVERT: D 275 LYS cc_start: 0.7186 (mttt) cc_final: 0.6410 (tptp) REVERT: D 437 ASN cc_start: 0.6345 (t0) cc_final: 0.5946 (m110) REVERT: D 451 LYS cc_start: 0.6760 (mmpt) cc_final: 0.6426 (mttt) outliers start: 28 outliers final: 11 residues processed: 192 average time/residue: 0.9590 time to fit residues: 206.6077 Evaluate side-chains 179 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13276 Z= 0.293 Angle : 0.629 15.589 18072 Z= 0.299 Chirality : 0.042 0.134 1992 Planarity : 0.005 0.049 2244 Dihedral : 5.271 59.921 1996 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.85 % Allowed : 14.24 % Favored : 83.90 % 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: 0.64 (0.22), residues: 1552 helix: 1.15 (0.17), residues: 988 sheet: 2.46 (0.92), residues: 40 loop : -1.11 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 392 HIS 0.003 0.001 HIS B 60 PHE 0.019 0.001 PHE B 56 TYR 0.009 0.001 TYR D 365 ARG 0.002 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.399 Fit side-chains REVERT: A 32 THR cc_start: 0.4092 (OUTLIER) cc_final: 0.3873 (p) REVERT: A 182 ASP cc_start: 0.6607 (t70) cc_final: 0.6145 (t70) REVERT: A 265 ILE cc_start: 0.7162 (mt) cc_final: 0.6745 (pt) REVERT: A 275 LYS cc_start: 0.7236 (mttt) cc_final: 0.6428 (tptp) REVERT: A 318 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6820 (mm) REVERT: A 437 ASN cc_start: 0.6399 (t0) cc_final: 0.5967 (m110) REVERT: A 451 LYS cc_start: 0.6742 (mmpt) cc_final: 0.6429 (mttt) REVERT: A 457 LYS cc_start: 0.5972 (pttt) cc_final: 0.5704 (tmtt) REVERT: B 32 THR cc_start: 0.4100 (OUTLIER) cc_final: 0.3897 (p) REVERT: B 182 ASP cc_start: 0.6640 (t70) cc_final: 0.6234 (t70) REVERT: B 275 LYS cc_start: 0.7259 (mttt) cc_final: 0.6458 (tptp) REVERT: B 437 ASN cc_start: 0.6387 (t0) cc_final: 0.5956 (m110) REVERT: B 451 LYS cc_start: 0.6747 (mmpt) cc_final: 0.6426 (mttt) REVERT: B 458 LYS cc_start: 0.6373 (mmmt) cc_final: 0.6142 (mtmt) REVERT: C 32 THR cc_start: 0.4077 (OUTLIER) cc_final: 0.3873 (p) REVERT: C 182 ASP cc_start: 0.6606 (t70) cc_final: 0.6143 (t70) REVERT: C 265 ILE cc_start: 0.7175 (mt) cc_final: 0.6852 (pt) REVERT: C 275 LYS cc_start: 0.7251 (mttt) cc_final: 0.6439 (tptp) REVERT: C 437 ASN cc_start: 0.6402 (t0) cc_final: 0.5988 (m-40) REVERT: C 451 LYS cc_start: 0.6732 (mmpt) cc_final: 0.6424 (mttt) REVERT: D 32 THR cc_start: 0.4088 (OUTLIER) cc_final: 0.3883 (p) REVERT: D 182 ASP cc_start: 0.6613 (t70) cc_final: 0.6145 (t70) REVERT: D 265 ILE cc_start: 0.7255 (mt) cc_final: 0.6886 (pt) REVERT: D 275 LYS cc_start: 0.7193 (mttt) cc_final: 0.6374 (tptp) REVERT: D 318 ILE cc_start: 0.7099 (tt) cc_final: 0.6828 (mm) REVERT: D 437 ASN cc_start: 0.6404 (t0) cc_final: 0.5973 (m110) REVERT: D 451 LYS cc_start: 0.6727 (mmpt) cc_final: 0.6417 (mttt) outliers start: 25 outliers final: 9 residues processed: 185 average time/residue: 1.0202 time to fit residues: 210.3558 Evaluate side-chains 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13276 Z= 0.316 Angle : 0.642 15.212 18072 Z= 0.310 Chirality : 0.043 0.155 1992 Planarity : 0.005 0.050 2244 Dihedral : 5.278 56.513 1996 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.85 % Allowed : 14.09 % Favored : 84.05 % 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: 0.40 (0.22), residues: 1552 helix: 1.00 (0.17), residues: 988 sheet: 2.32 (0.90), residues: 40 loop : -1.29 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 392 HIS 0.004 0.001 HIS A 60 PHE 0.019 0.002 PHE A 56 TYR 0.010 0.001 TYR A 365 ARG 0.002 0.000 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.405 Fit side-chains REVERT: A 32 THR cc_start: 0.4246 (OUTLIER) cc_final: 0.4021 (p) REVERT: A 182 ASP cc_start: 0.6608 (t70) cc_final: 0.6149 (t70) REVERT: A 275 LYS cc_start: 0.7276 (mttt) cc_final: 0.6435 (tptp) REVERT: A 318 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6886 (mm) REVERT: A 437 ASN cc_start: 0.6276 (t0) cc_final: 0.5886 (m110) REVERT: A 451 LYS cc_start: 0.6706 (mmpt) cc_final: 0.6426 (mttt) REVERT: B 32 THR cc_start: 0.4286 (OUTLIER) cc_final: 0.4070 (p) REVERT: B 182 ASP cc_start: 0.6603 (t70) cc_final: 0.6204 (t70) REVERT: B 275 LYS cc_start: 0.7291 (mttt) cc_final: 0.6475 (tptp) REVERT: B 437 ASN cc_start: 0.6264 (t0) cc_final: 0.5881 (m110) REVERT: B 451 LYS cc_start: 0.6717 (mmpt) cc_final: 0.6415 (mttt) REVERT: B 458 LYS cc_start: 0.6383 (mmmt) cc_final: 0.6128 (mtmt) REVERT: C 32 THR cc_start: 0.4267 (OUTLIER) cc_final: 0.4051 (p) REVERT: C 182 ASP cc_start: 0.6614 (t70) cc_final: 0.6153 (t70) REVERT: C 275 LYS cc_start: 0.7277 (mttt) cc_final: 0.6468 (tptp) REVERT: C 437 ASN cc_start: 0.6277 (t0) cc_final: 0.5896 (m110) REVERT: C 451 LYS cc_start: 0.6615 (mmpt) cc_final: 0.6354 (mttt) REVERT: D 32 THR cc_start: 0.4276 (OUTLIER) cc_final: 0.4060 (p) REVERT: D 182 ASP cc_start: 0.6614 (t70) cc_final: 0.6156 (t70) REVERT: D 275 LYS cc_start: 0.7285 (mttt) cc_final: 0.6442 (tptp) REVERT: D 318 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6890 (mm) REVERT: D 437 ASN cc_start: 0.6279 (t0) cc_final: 0.5896 (m110) REVERT: D 451 LYS cc_start: 0.6695 (mmpt) cc_final: 0.6412 (mttt) REVERT: D 457 LYS cc_start: 0.5974 (pttt) cc_final: 0.5669 (tmtt) outliers start: 25 outliers final: 15 residues processed: 174 average time/residue: 0.9608 time to fit residues: 187.0366 Evaluate side-chains 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 382 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13276 Z= 0.201 Angle : 0.580 15.422 18072 Z= 0.279 Chirality : 0.040 0.154 1992 Planarity : 0.004 0.048 2244 Dihedral : 4.744 56.180 1996 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.63 % Allowed : 14.84 % Favored : 83.53 % 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: 0.65 (0.22), residues: 1552 helix: 1.19 (0.17), residues: 984 sheet: 2.42 (0.92), residues: 40 loop : -1.17 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 392 HIS 0.002 0.001 HIS B 60 PHE 0.019 0.001 PHE B 56 TYR 0.006 0.001 TYR A 48 ARG 0.001 0.000 ARG C 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.426 Fit side-chains REVERT: A 32 THR cc_start: 0.4262 (OUTLIER) cc_final: 0.4004 (p) REVERT: A 182 ASP cc_start: 0.6585 (t70) cc_final: 0.6128 (t70) REVERT: A 265 ILE cc_start: 0.7164 (mt) cc_final: 0.6800 (pt) REVERT: A 275 LYS cc_start: 0.7296 (mttt) cc_final: 0.6477 (tptp) REVERT: A 318 ILE cc_start: 0.7104 (tt) cc_final: 0.6884 (mm) REVERT: A 437 ASN cc_start: 0.6294 (t0) cc_final: 0.5913 (m-40) REVERT: A 451 LYS cc_start: 0.6718 (mmpt) cc_final: 0.6427 (mtmt) REVERT: B 32 THR cc_start: 0.4289 (OUTLIER) cc_final: 0.4041 (p) REVERT: B 182 ASP cc_start: 0.6562 (t70) cc_final: 0.6134 (t70) REVERT: B 265 ILE cc_start: 0.7199 (mt) cc_final: 0.6835 (pt) REVERT: B 275 LYS cc_start: 0.7306 (mttt) cc_final: 0.6503 (tptp) REVERT: B 437 ASN cc_start: 0.6360 (t0) cc_final: 0.5965 (m-40) REVERT: B 451 LYS cc_start: 0.6711 (mmpt) cc_final: 0.6408 (mttt) REVERT: B 458 LYS cc_start: 0.6401 (mmmt) cc_final: 0.6133 (mtmt) REVERT: C 32 THR cc_start: 0.4240 (OUTLIER) cc_final: 0.4000 (p) REVERT: C 182 ASP cc_start: 0.6590 (t70) cc_final: 0.6133 (t70) REVERT: C 265 ILE cc_start: 0.7118 (mt) cc_final: 0.6800 (pt) REVERT: C 275 LYS cc_start: 0.7286 (mttt) cc_final: 0.6477 (tptp) REVERT: C 437 ASN cc_start: 0.6299 (t0) cc_final: 0.5911 (m-40) REVERT: C 451 LYS cc_start: 0.6669 (mmpt) cc_final: 0.6406 (mtmt) REVERT: D 32 THR cc_start: 0.4249 (OUTLIER) cc_final: 0.4011 (p) REVERT: D 182 ASP cc_start: 0.6597 (t70) cc_final: 0.6141 (t70) REVERT: D 265 ILE cc_start: 0.7179 (mt) cc_final: 0.6809 (pt) REVERT: D 275 LYS cc_start: 0.7279 (mttt) cc_final: 0.6470 (tptp) REVERT: D 318 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6901 (mm) REVERT: D 437 ASN cc_start: 0.6321 (t0) cc_final: 0.5932 (m-40) REVERT: D 451 LYS cc_start: 0.6694 (mmpt) cc_final: 0.6409 (mttt) outliers start: 22 outliers final: 12 residues processed: 165 average time/residue: 1.0718 time to fit residues: 196.5204 Evaluate side-chains 170 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 406 MET Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 406 MET Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.198965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138532 restraints weight = 14369.665| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.95 r_work: 0.3228 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13276 Z= 0.199 Angle : 0.578 15.310 18072 Z= 0.278 Chirality : 0.040 0.158 1992 Planarity : 0.004 0.048 2244 Dihedral : 4.470 48.432 1996 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.93 % Allowed : 14.61 % Favored : 83.46 % 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: 0.78 (0.22), residues: 1552 helix: 1.27 (0.17), residues: 980 sheet: 2.31 (0.91), residues: 40 loop : -1.00 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 392 HIS 0.002 0.001 HIS A 60 PHE 0.019 0.001 PHE A 266 TYR 0.007 0.001 TYR D 365 ARG 0.001 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.77 seconds wall clock time: 75 minutes 55.83 seconds (4555.83 seconds total)