Starting phenix.real_space_refine on Wed Mar 20 12:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhr_16067/03_2024/8bhr_16067_trim_updated.pdb" } resolution = 3.38 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8945 2.51 5 N 2280 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27215 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QM7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QM7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QM7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QM7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QM7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.16, per 1000 atoms: 0.45 Number of scatterers: 27215 At special positions: 0 Unit cell: (92.02, 95.23, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2490 8.00 N 2280 7.00 C 8945 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 21.58 Conformation dependent library (CDL) restraints added in 2.6 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 36.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.543A pdb=" N VAL A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 3.541A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 311 Processing helix chain 'A' and resid 318 through 418 removed outlier: 3.592A pdb=" N LYS A 393 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.543A pdb=" N VAL B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 3.542A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 318 through 418 removed outlier: 3.592A pdb=" N LYS B 393 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 178 through 181 No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 3.543A pdb=" N VAL C 246 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 3.541A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 311 Processing helix chain 'C' and resid 318 through 418 removed outlier: 3.593A pdb=" N LYS C 393 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 178 through 181 No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 3.543A pdb=" N VAL D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 3.541A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 318 through 418 removed outlier: 3.592A pdb=" N LYS D 393 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 3.543A pdb=" N VAL E 246 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 3.542A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 311 Processing helix chain 'E' and resid 318 through 418 removed outlier: 3.592A pdb=" N LYS E 393 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 7.054A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.860A pdb=" N MET A 48 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.573A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.564A pdb=" N MET A 121 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 133 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 7.054A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.861A pdb=" N MET B 48 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.573A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.565A pdb=" N MET B 121 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 133 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 170 through 174 removed outlier: 7.054A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 182 through 184 removed outlier: 6.862A pdb=" N MET C 48 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.572A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.564A pdb=" N MET C 121 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 133 " --> pdb=" O MET C 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 170 through 174 removed outlier: 7.053A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 182 through 184 removed outlier: 6.861A pdb=" N MET D 48 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.573A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.564A pdb=" N MET D 121 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 133 " --> pdb=" O MET D 121 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 170 through 174 removed outlier: 7.053A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 182 through 184 removed outlier: 6.861A pdb=" N MET E 48 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.573A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 120 through 124 removed outlier: 3.564A pdb=" N MET E 121 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 133 " --> pdb=" O MET E 121 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1647 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: 9.83 Time building geometry restraints manager: 22.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 5 1.23 - 1.42: 6130 1.42 - 1.62: 7885 1.62 - 1.81: 150 Bond restraints: 27585 Sorted by residual: bond pdb=" N QM7 A 502 " pdb=" C5 QM7 A 502 " ideal model delta sigma weight residual 1.453 1.339 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" N QM7 E 502 " pdb=" C5 QM7 E 502 " ideal model delta sigma weight residual 1.453 1.339 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" N QM7 C 502 " pdb=" C5 QM7 C 502 " ideal model delta sigma weight residual 1.453 1.340 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" N QM7 D 502 " pdb=" C5 QM7 D 502 " ideal model delta sigma weight residual 1.453 1.340 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" N QM7 B 502 " pdb=" C5 QM7 B 502 " ideal model delta sigma weight residual 1.453 1.340 0.113 2.00e-02 2.50e+03 3.18e+01 ... (remaining 27580 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 471 107.09 - 113.82: 32016 113.82 - 120.55: 9457 120.55 - 127.27: 7416 127.27 - 134.00: 190 Bond angle restraints: 49550 Sorted by residual: angle pdb=" C11 QM7 C 502 " pdb=" C14 QM7 C 502 " pdb=" C15 QM7 C 502 " ideal model delta sigma weight residual 153.90 129.52 24.38 3.00e+00 1.11e-01 6.60e+01 angle pdb=" C11 QM7 E 502 " pdb=" C14 QM7 E 502 " pdb=" C15 QM7 E 502 " ideal model delta sigma weight residual 153.90 129.52 24.38 3.00e+00 1.11e-01 6.60e+01 angle pdb=" C11 QM7 B 502 " pdb=" C14 QM7 B 502 " pdb=" C15 QM7 B 502 " ideal model delta sigma weight residual 153.90 129.55 24.35 3.00e+00 1.11e-01 6.59e+01 angle pdb=" C11 QM7 D 502 " pdb=" C14 QM7 D 502 " pdb=" C15 QM7 D 502 " ideal model delta sigma weight residual 153.90 129.56 24.34 3.00e+00 1.11e-01 6.58e+01 angle pdb=" C11 QM7 A 502 " pdb=" C14 QM7 A 502 " pdb=" C15 QM7 A 502 " ideal model delta sigma weight residual 153.90 129.59 24.31 3.00e+00 1.11e-01 6.57e+01 ... (remaining 49545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.58: 12214 11.58 - 23.16: 611 23.16 - 34.74: 120 34.74 - 46.31: 75 46.31 - 57.89: 120 Dihedral angle restraints: 13140 sinusoidal: 7010 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.12 -41.12 3 1.50e+01 4.44e-03 7.35e+00 dihedral pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " pdb=" CD LYS A 315 " pdb=" CE LYS A 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.12 -41.12 3 1.50e+01 4.44e-03 7.35e+00 dihedral pdb=" CB LYS E 315 " pdb=" CG LYS E 315 " pdb=" CD LYS E 315 " pdb=" CE LYS E 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.11 -41.11 3 1.50e+01 4.44e-03 7.35e+00 ... (remaining 13137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1415 0.028 - 0.056: 475 0.056 - 0.085: 156 0.085 - 0.113: 106 0.113 - 0.141: 13 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C3 QM7 E 502 " pdb=" N QM7 E 502 " pdb=" C2 QM7 E 502 " pdb=" C4 QM7 E 502 " both_signs ideal model delta sigma weight residual False -2.61 -2.47 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" C3 QM7 A 502 " pdb=" N QM7 A 502 " pdb=" C2 QM7 A 502 " pdb=" C4 QM7 A 502 " both_signs ideal model delta sigma weight residual False -2.61 -2.47 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" C3 QM7 D 502 " pdb=" N QM7 D 502 " pdb=" C2 QM7 D 502 " pdb=" C4 QM7 D 502 " both_signs ideal model delta sigma weight residual False -2.61 -2.47 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 2162 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N QM7 B 502 " 0.379 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" C3 QM7 B 502 " -0.269 2.00e-02 2.50e+03 pdb=" C5 QM7 B 502 " 0.072 2.00e-02 2.50e+03 pdb=" C6 QM7 B 502 " -0.181 2.00e-02 2.50e+03 pdb=" O1 QM7 B 502 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N QM7 C 502 " 0.378 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" C3 QM7 C 502 " -0.269 2.00e-02 2.50e+03 pdb=" C5 QM7 C 502 " 0.072 2.00e-02 2.50e+03 pdb=" C6 QM7 C 502 " -0.181 2.00e-02 2.50e+03 pdb=" O1 QM7 C 502 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N QM7 A 502 " 0.378 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" C3 QM7 A 502 " -0.269 2.00e-02 2.50e+03 pdb=" C5 QM7 A 502 " 0.072 2.00e-02 2.50e+03 pdb=" C6 QM7 A 502 " -0.181 2.00e-02 2.50e+03 pdb=" O1 QM7 A 502 " -0.000 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 10859 2.39 - 2.94: 59898 2.94 - 3.50: 65946 3.50 - 4.05: 91031 4.05 - 4.60: 137268 Nonbonded interactions: 365002 Sorted by model distance: nonbonded pdb=" HG1 THR A 210 " pdb=" OH TYR A 213 " model vdw 1.838 1.850 nonbonded pdb=" HG1 THR E 210 " pdb=" OH TYR E 213 " model vdw 1.838 1.850 nonbonded pdb=" HG1 THR D 210 " pdb=" OH TYR D 213 " model vdw 1.839 1.850 nonbonded pdb=" OE1 GLN B 71 " pdb=" HG1 THR B 102 " model vdw 1.839 1.850 nonbonded pdb=" HG1 THR B 210 " pdb=" OH TYR B 213 " model vdw 1.839 1.850 ... (remaining 364997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.380 Extract box with map and model: 4.580 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 84.550 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 0.114 14170 Z= 0.293 Angle : 0.803 24.379 19275 Z= 0.298 Chirality : 0.038 0.141 2165 Planarity : 0.011 0.225 2395 Dihedral : 7.330 57.703 5130 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.26 (0.22), residues: 1670 helix: 3.22 (0.22), residues: 575 sheet: 0.47 (0.28), residues: 390 loop : 0.76 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 73 HIS 0.003 0.001 HIS C 195 PHE 0.005 0.001 PHE D 149 TYR 0.006 0.001 TYR D 285 ARG 0.002 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8335 (mmm) cc_final: 0.8033 (mtm) REVERT: B 101 ASP cc_start: 0.8168 (p0) cc_final: 0.7501 (t0) REVERT: B 413 TYR cc_start: 0.8322 (t80) cc_final: 0.7920 (t80) REVERT: C 101 ASP cc_start: 0.8254 (p0) cc_final: 0.7691 (t0) REVERT: D 101 ASP cc_start: 0.8242 (p0) cc_final: 0.7587 (t0) REVERT: D 151 MET cc_start: 0.7502 (mpt) cc_final: 0.7163 (mpt) REVERT: D 297 TYR cc_start: 0.8223 (t80) cc_final: 0.7606 (t80) REVERT: E 101 ASP cc_start: 0.8249 (p0) cc_final: 0.7652 (t0) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.6706 time to fit residues: 340.5235 Evaluate side-chains 249 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 167 ASN B 219 HIS B 311 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 219 HIS C 311 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN E 167 ASN E 219 HIS E 311 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 14170 Z= 0.417 Angle : 0.595 4.787 19275 Z= 0.320 Chirality : 0.044 0.155 2165 Planarity : 0.005 0.042 2395 Dihedral : 5.383 50.825 1995 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.61 % Allowed : 6.64 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.18 (0.20), residues: 1670 helix: 2.37 (0.20), residues: 555 sheet: -0.19 (0.24), residues: 520 loop : 0.33 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 414 HIS 0.005 0.002 HIS C 113 PHE 0.017 0.002 PHE A 68 TYR 0.015 0.002 TYR C 132 ARG 0.004 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8540 (mmm) cc_final: 0.8274 (mtm) REVERT: B 20 ARG cc_start: 0.6619 (mtt-85) cc_final: 0.6399 (mtm-85) REVERT: C 20 ARG cc_start: 0.6897 (mtt-85) cc_final: 0.6656 (mtm-85) REVERT: C 397 MET cc_start: 0.7984 (mmt) cc_final: 0.7590 (mmp) outliers start: 24 outliers final: 18 residues processed: 246 average time/residue: 0.6927 time to fit residues: 234.1954 Evaluate side-chains 183 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 167 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 251 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14170 Z= 0.213 Angle : 0.472 4.723 19275 Z= 0.249 Chirality : 0.040 0.139 2165 Planarity : 0.004 0.038 2395 Dihedral : 5.088 54.990 1995 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.34 % Allowed : 9.46 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.26 (0.21), residues: 1670 helix: 2.39 (0.22), residues: 555 sheet: 0.02 (0.25), residues: 430 loop : 0.19 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 414 HIS 0.003 0.001 HIS C 195 PHE 0.011 0.002 PHE E 68 TYR 0.008 0.001 TYR D 132 ARG 0.003 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8534 (mmm) cc_final: 0.8173 (mtm) REVERT: A 223 LYS cc_start: 0.8839 (tttt) cc_final: 0.8608 (ttpt) REVERT: A 297 TYR cc_start: 0.8606 (t80) cc_final: 0.8296 (t80) REVERT: C 397 MET cc_start: 0.7923 (mmt) cc_final: 0.7600 (mmp) REVERT: D 239 MET cc_start: 0.9034 (mmp) cc_final: 0.8713 (mmt) REVERT: D 297 TYR cc_start: 0.8507 (t80) cc_final: 0.7894 (t80) REVERT: D 302 SER cc_start: 0.8933 (m) cc_final: 0.8723 (m) outliers start: 20 outliers final: 18 residues processed: 195 average time/residue: 0.6257 time to fit residues: 172.8161 Evaluate side-chains 194 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 251 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14170 Z= 0.275 Angle : 0.483 4.443 19275 Z= 0.255 Chirality : 0.041 0.145 2165 Planarity : 0.004 0.041 2395 Dihedral : 5.424 58.568 1995 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.95 % Allowed : 8.99 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.89 (0.20), residues: 1670 helix: 1.96 (0.22), residues: 575 sheet: -0.10 (0.25), residues: 430 loop : -0.04 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 414 HIS 0.004 0.001 HIS C 195 PHE 0.013 0.002 PHE A 68 TYR 0.010 0.001 TYR D 132 ARG 0.003 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8488 (mmm) cc_final: 0.8178 (mtm) REVERT: A 223 LYS cc_start: 0.8872 (tttt) cc_final: 0.8658 (ttpt) REVERT: C 144 MET cc_start: 0.8663 (mtm) cc_final: 0.8453 (mtt) REVERT: C 397 MET cc_start: 0.7862 (mmt) cc_final: 0.7553 (mmp) REVERT: D 297 TYR cc_start: 0.8622 (t80) cc_final: 0.8046 (t80) REVERT: D 302 SER cc_start: 0.8910 (m) cc_final: 0.8700 (m) outliers start: 29 outliers final: 28 residues processed: 198 average time/residue: 0.6644 time to fit residues: 189.0228 Evaluate side-chains 207 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14170 Z= 0.206 Angle : 0.447 4.853 19275 Z= 0.233 Chirality : 0.039 0.137 2165 Planarity : 0.004 0.063 2395 Dihedral : 5.002 52.046 1995 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.81 % Allowed : 9.40 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.20), residues: 1670 helix: 2.05 (0.22), residues: 575 sheet: -0.13 (0.24), residues: 450 loop : 0.01 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 414 HIS 0.003 0.001 HIS C 195 PHE 0.011 0.001 PHE C 68 TYR 0.007 0.001 TYR D 132 ARG 0.008 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8508 (mmm) cc_final: 0.8110 (mtm) REVERT: C 144 MET cc_start: 0.8698 (mtm) cc_final: 0.8440 (mtt) REVERT: C 397 MET cc_start: 0.7891 (mmt) cc_final: 0.7581 (mmp) REVERT: D 297 TYR cc_start: 0.8593 (t80) cc_final: 0.7966 (t80) REVERT: D 302 SER cc_start: 0.8905 (m) cc_final: 0.8703 (m) outliers start: 27 outliers final: 24 residues processed: 208 average time/residue: 0.6112 time to fit residues: 181.7412 Evaluate side-chains 189 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14170 Z= 0.364 Angle : 0.524 5.087 19275 Z= 0.276 Chirality : 0.042 0.148 2165 Planarity : 0.004 0.044 2395 Dihedral : 5.891 52.616 1995 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.82 % Allowed : 9.26 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.52 (0.20), residues: 1670 helix: 1.72 (0.22), residues: 575 sheet: -0.50 (0.24), residues: 465 loop : -0.13 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 414 HIS 0.004 0.001 HIS C 195 PHE 0.015 0.002 PHE B 68 TYR 0.011 0.002 TYR D 132 ARG 0.003 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8483 (mmm) cc_final: 0.8186 (mtm) REVERT: C 144 MET cc_start: 0.8697 (mtm) cc_final: 0.8450 (mtt) REVERT: C 397 MET cc_start: 0.7911 (mmt) cc_final: 0.7598 (mmp) REVERT: E 20 ARG cc_start: 0.6893 (mtt-85) cc_final: 0.6563 (mtm-85) outliers start: 42 outliers final: 39 residues processed: 196 average time/residue: 0.6165 time to fit residues: 171.6834 Evaluate side-chains 199 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14170 Z= 0.224 Angle : 0.459 4.568 19275 Z= 0.238 Chirality : 0.040 0.140 2165 Planarity : 0.004 0.042 2395 Dihedral : 5.554 58.660 1995 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.69 (0.21), residues: 1670 helix: 1.90 (0.22), residues: 575 sheet: -0.43 (0.24), residues: 455 loop : -0.06 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS C 195 PHE 0.014 0.001 PHE D 409 TYR 0.008 0.001 TYR C 285 ARG 0.003 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8477 (mmm) cc_final: 0.8117 (mtm) REVERT: C 144 MET cc_start: 0.8681 (mtm) cc_final: 0.8420 (mtt) REVERT: C 397 MET cc_start: 0.7863 (mmt) cc_final: 0.7598 (mmp) REVERT: E 20 ARG cc_start: 0.6844 (mtt-85) cc_final: 0.6556 (mtm-85) outliers start: 31 outliers final: 31 residues processed: 183 average time/residue: 0.6511 time to fit residues: 169.8714 Evaluate side-chains 192 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14170 Z= 0.293 Angle : 0.490 5.806 19275 Z= 0.255 Chirality : 0.040 0.147 2165 Planarity : 0.004 0.043 2395 Dihedral : 5.919 55.106 1995 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.55 % Allowed : 9.80 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.54 (0.20), residues: 1670 helix: 1.82 (0.22), residues: 575 sheet: -0.55 (0.23), residues: 465 loop : -0.15 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 414 HIS 0.004 0.001 HIS C 195 PHE 0.014 0.002 PHE D 409 TYR 0.009 0.001 TYR B 285 ARG 0.003 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8485 (mmm) cc_final: 0.8143 (mtm) REVERT: C 61 MET cc_start: 0.8352 (mmm) cc_final: 0.8090 (mtt) REVERT: C 144 MET cc_start: 0.8681 (mtm) cc_final: 0.8384 (mtt) REVERT: C 397 MET cc_start: 0.7879 (mmt) cc_final: 0.7608 (mmp) outliers start: 38 outliers final: 38 residues processed: 187 average time/residue: 0.6055 time to fit residues: 163.0043 Evaluate side-chains 198 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14170 Z= 0.219 Angle : 0.459 5.568 19275 Z= 0.237 Chirality : 0.040 0.138 2165 Planarity : 0.004 0.042 2395 Dihedral : 5.794 59.393 1995 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.15 % Allowed : 10.13 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.70 (0.21), residues: 1670 helix: 1.96 (0.22), residues: 575 sheet: -0.46 (0.24), residues: 455 loop : -0.08 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 414 HIS 0.003 0.001 HIS C 195 PHE 0.014 0.001 PHE D 409 TYR 0.008 0.001 TYR C 285 ARG 0.003 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8501 (mmm) cc_final: 0.8078 (mtm) REVERT: C 58 ASP cc_start: 0.7472 (m-30) cc_final: 0.7220 (m-30) REVERT: C 397 MET cc_start: 0.7894 (mmt) cc_final: 0.7631 (mmp) outliers start: 32 outliers final: 32 residues processed: 180 average time/residue: 0.6124 time to fit residues: 157.2358 Evaluate side-chains 190 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8318 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14170 Z= 0.215 Angle : 0.460 5.903 19275 Z= 0.236 Chirality : 0.040 0.142 2165 Planarity : 0.004 0.042 2395 Dihedral : 5.639 55.593 1995 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.21 % Allowed : 10.13 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.73 (0.21), residues: 1670 helix: 2.00 (0.22), residues: 575 sheet: -0.46 (0.24), residues: 455 loop : -0.07 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 114 HIS 0.003 0.001 HIS C 195 PHE 0.014 0.001 PHE D 409 TYR 0.007 0.001 TYR C 285 ARG 0.003 0.000 ARG D 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8498 (mmm) cc_final: 0.8074 (mtm) REVERT: C 397 MET cc_start: 0.7883 (mmt) cc_final: 0.7622 (mmp) outliers start: 33 outliers final: 33 residues processed: 181 average time/residue: 0.6164 time to fit residues: 159.1537 Evaluate side-chains 192 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 278 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.104386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.086748 restraints weight = 59095.262| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.98 r_work: 0.2862 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 14170 Z= 0.298 Angle : 0.494 6.168 19275 Z= 0.256 Chirality : 0.040 0.149 2165 Planarity : 0.004 0.043 2395 Dihedral : 5.917 57.941 1995 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 9.60 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.54 (0.20), residues: 1670 helix: 1.87 (0.22), residues: 575 sheet: -0.59 (0.23), residues: 465 loop : -0.16 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 414 HIS 0.004 0.001 HIS C 195 PHE 0.014 0.002 PHE D 409 TYR 0.009 0.001 TYR B 285 ARG 0.004 0.000 ARG B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5657.08 seconds wall clock time: 100 minutes 42.77 seconds (6042.77 seconds total)