Starting phenix.real_space_refine on Fri Sep 27 11:17:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/09_2024/7pbd_13290.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/09_2024/7pbd_13290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/09_2024/7pbd_13290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/09_2024/7pbd_13290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/09_2024/7pbd_13290.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbd_13290/09_2024/7pbd_13290.cif" } resolution = 3.04 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 893 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9617 2.51 5 N 2423 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2749 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 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: 9.64, per 1000 atoms: 0.65 Number of scatterers: 14822 At special positions: 0 Unit cell: (94.5, 120.75, 135.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2698 8.00 N 2423 7.00 C 9617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM14820 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14777 O5 NAG A 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 802 " - " ASN A 111 " " NAG D 502 " - " ASN D 111 " " NAG E 501 " - " ASN E 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN C 80 " " NAG K 1 " - " ASN E 149 " Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 1.8 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 40.6% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.608A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.866A pdb=" N SER A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 93' Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.600A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 4.127A pdb=" N VAL A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 619 through 645 removed outlier: 4.110A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 682 removed outlier: 4.772A pdb=" N LYS A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 715 removed outlier: 3.755A pdb=" N LYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Proline residue: A 698 - end of helix removed outlier: 3.678A pdb=" N ARG A 715 " --> pdb=" O THR A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.530A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 239 removed outlier: 5.133A pdb=" N MET B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix removed outlier: 4.024A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 246 through 269 removed outlier: 3.590A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 415 through 447 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.548A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.938A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 268 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 279 through 308 removed outlier: 3.703A pdb=" N ALA C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 447 removed outlier: 3.798A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.550A pdb=" N LEU E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.027A pdb=" N GLN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.356A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 243 removed outlier: 4.870A pdb=" N MET E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix removed outlier: 4.512A pdb=" N ASN E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 270 removed outlier: 3.954A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 416 through 447 Proline residue: E 432 - end of helix Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.753A pdb=" N SER D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.488A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 223 through 230 removed outlier: 4.157A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 247 Processing helix chain 'D' and resid 251 through 276 removed outlier: 3.598A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.130A pdb=" N ALA D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Proline residue: D 330 - end of helix removed outlier: 3.734A pdb=" N ASN D 346 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 418 Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 474 through 478 removed outlier: 3.665A pdb=" N THR F 478 " --> pdb=" O PRO F 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 44 current: chain 'A' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.247A pdb=" N SER A 159 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 579 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 195 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 588 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 193 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 46 current: chain 'B' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.824A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR B 205 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 197 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG B 207 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 195 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 209 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 193 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER B 211 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS B 191 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG B 213 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.622A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.994A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR C 205 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 207 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER C 211 " --> pdb=" O HIS C 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 46 current: chain 'E' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.802A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 39 through 54 removed outlier: 6.257A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.023A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AB3, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB4, first strand: chain 'F' and resid 421 through 426 removed outlier: 6.514A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 445 through 447 current: chain 'F' and resid 501 through 502 592 hydrogen bonds defined for protein. 1701 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: 4.28 Time building geometry restraints manager: 4.75 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: 4532 1.34 - 1.46: 4052 1.46 - 1.58: 6469 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15199 Sorted by residual: bond pdb=" CG HSM B 601 " pdb=" ND1 HSM B 601 " ideal model delta sigma weight residual 1.383 1.312 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CD2 HSM B 601 " pdb=" NE2 HSM B 601 " ideal model delta sigma weight residual 1.376 1.313 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" N ILE C 423 " pdb=" CA ILE C 423 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.00e+00 bond pdb=" N TRP C 426 " pdb=" CA TRP C 426 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.21e-02 6.83e+03 4.79e+00 ... (remaining 15194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 20078 1.97 - 3.94: 431 3.94 - 5.91: 116 5.91 - 7.88: 30 7.88 - 9.85: 2 Bond angle restraints: 20657 Sorted by residual: angle pdb=" N ILE E 281 " pdb=" CA ILE E 281 " pdb=" C ILE E 281 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" N ALA C 420 " pdb=" CA ALA C 420 " pdb=" C ALA C 420 " ideal model delta sigma weight residual 112.93 107.44 5.49 1.33e+00 5.65e-01 1.70e+01 angle pdb=" C LYS F 452 " pdb=" N ASP F 453 " pdb=" CA ASP F 453 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N ALA C 421 " pdb=" CA ALA C 421 " pdb=" C ALA C 421 " ideal model delta sigma weight residual 111.75 106.95 4.80 1.28e+00 6.10e-01 1.41e+01 angle pdb=" CA ASP F 453 " pdb=" CB ASP F 453 " pdb=" CG ASP F 453 " ideal model delta sigma weight residual 112.60 116.09 -3.49 1.00e+00 1.00e+00 1.22e+01 ... (remaining 20652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 8648 23.44 - 46.89: 447 46.89 - 70.33: 37 70.33 - 93.77: 29 93.77 - 117.22: 43 Dihedral angle restraints: 9204 sinusoidal: 3938 harmonic: 5266 Sorted by residual: dihedral pdb=" CB CYS D 139 " pdb=" SG CYS D 139 " pdb=" SG CYS D 153 " pdb=" CB CYS D 153 " ideal model delta sinusoidal sigma weight residual 93.00 42.28 50.72 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA CYS E 150 " pdb=" C CYS E 150 " pdb=" N THR E 151 " pdb=" CA THR E 151 " ideal model delta harmonic sigma weight residual 180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N GLU B 153 " pdb=" CA GLU B 153 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 9201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.450: 2374 0.450 - 0.901: 8 0.901 - 1.351: 1 1.351 - 1.802: 2 1.802 - 2.252: 2 Chirality restraints: 2387 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.15 -2.25 2.00e-02 2.50e+03 1.27e+04 chirality pdb=" C1 MAN H 5 " pdb=" O6 BMA H 3 " pdb=" C2 MAN H 5 " pdb=" O5 MAN H 5 " both_signs ideal model delta sigma weight residual False 2.40 0.45 1.95 2.00e-02 2.50e+03 9.47e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.64 -1.76 2.00e-02 2.50e+03 7.76e+03 ... (remaining 2384 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " -0.132 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" CG ASN C 80 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " 0.513 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 80 " 0.238 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" CG ASN E 80 " -0.116 2.00e-02 2.50e+03 pdb=" OD1 ASN E 80 " -0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN E 80 " -0.365 2.00e-02 2.50e+03 pdb=" C1 NAG E 501 " 0.309 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " 0.137 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN C 149 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " -0.218 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.179 2.00e-02 2.50e+03 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 173 2.63 - 3.20: 13593 3.20 - 3.76: 22774 3.76 - 4.33: 32017 4.33 - 4.90: 53293 Nonbonded interactions: 121850 Sorted by model distance: nonbonded pdb=" OE2 GLU B 179 " pdb=" OG SER F 446 " model vdw 2.062 3.040 nonbonded pdb=" OH TYR B 97 " pdb=" OE2 GLU B 155 " model vdw 2.090 3.040 nonbonded pdb=" O TYR B 304 " pdb=" OG SER B 308 " model vdw 2.179 3.040 nonbonded pdb=" ND2 ASN D 88 " pdb=" O PRO D 115 " model vdw 2.203 3.120 nonbonded pdb=" OE2 GLU B 153 " pdb=" NE ARG B 207 " model vdw 2.206 3.120 ... (remaining 121845 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' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 8 through 308 or resid 419 through 447)) selection = chain 'C' selection = (chain 'E' and (resid 8 through 308 or resid 419 through 447)) } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' } 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.070 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.005 0.071 15199 Z= 0.298 Angle : 0.758 9.846 20657 Z= 0.380 Chirality : 0.101 2.252 2387 Planarity : 0.004 0.052 2536 Dihedral : 16.572 117.217 5802 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.14 (0.21), residues: 1764 helix: 1.63 (0.22), residues: 595 sheet: -0.66 (0.24), residues: 461 loop : -0.61 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.006 0.001 HIS D 110 PHE 0.023 0.002 PHE A 626 TYR 0.013 0.001 TYR E 157 ARG 0.009 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.783 Fit side-chains revert: symmetry clash REVERT: A 597 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 227 MET cc_start: 0.7754 (ppp) cc_final: 0.7422 (ppp) REVERT: C 49 MET cc_start: 0.8388 (ppp) cc_final: 0.7889 (ppp) REVERT: C 90 GLN cc_start: 0.8881 (mp10) cc_final: 0.8574 (mp10) REVERT: E 49 MET cc_start: 0.8276 (mmm) cc_final: 0.7839 (tmm) REVERT: E 282 ASP cc_start: 0.8718 (m-30) cc_final: 0.8505 (t70) REVERT: E 283 MET cc_start: 0.8339 (ttt) cc_final: 0.8114 (ttm) REVERT: D 228 ILE cc_start: 0.9177 (tt) cc_final: 0.8814 (tt) REVERT: F 3 GLN cc_start: 0.8089 (mp10) cc_final: 0.7597 (mp10) REVERT: F 5 GLN cc_start: 0.8079 (mp-120) cc_final: 0.7829 (mm-40) REVERT: F 6 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6684 (tm-30) REVERT: F 405 LEU cc_start: 0.6888 (tt) cc_final: 0.6553 (tp) REVERT: F 412 SER cc_start: 0.8232 (p) cc_final: 0.7515 (p) REVERT: F 414 HIS cc_start: 0.8172 (m90) cc_final: 0.7690 (m90) REVERT: F 456 THR cc_start: 0.9067 (m) cc_final: 0.8406 (p) REVERT: F 470 MET cc_start: 0.8381 (mpp) cc_final: 0.7838 (mpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2272 time to fit residues: 61.1127 Evaluate side-chains 135 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 0.0570 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN D 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15199 Z= 0.352 Angle : 0.655 11.704 20657 Z= 0.323 Chirality : 0.047 0.346 2387 Planarity : 0.004 0.041 2536 Dihedral : 12.147 128.697 2453 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.63 % Allowed : 6.51 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.25 (0.21), residues: 1764 helix: 1.81 (0.21), residues: 596 sheet: -0.75 (0.23), residues: 462 loop : -0.52 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 241 HIS 0.003 0.001 HIS B 119 PHE 0.022 0.002 PHE E 186 TYR 0.017 0.001 TYR B 299 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.812 Fit side-chains REVERT: A 597 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 227 MET cc_start: 0.8042 (ppp) cc_final: 0.7397 (ppp) REVERT: C 49 MET cc_start: 0.8306 (ppp) cc_final: 0.7890 (ppp) REVERT: C 155 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7478 (mm-30) REVERT: E 49 MET cc_start: 0.8240 (mmm) cc_final: 0.7793 (tmm) REVERT: E 55 MET cc_start: 0.8762 (mmm) cc_final: 0.8390 (mmm) REVERT: E 185 GLN cc_start: 0.8945 (pm20) cc_final: 0.8637 (pm20) REVERT: D 213 MET cc_start: 0.8615 (mtm) cc_final: 0.8409 (mtm) REVERT: D 229 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8326 (tp-100) REVERT: F 414 HIS cc_start: 0.8130 (m90) cc_final: 0.7684 (m90) REVERT: F 456 THR cc_start: 0.8982 (m) cc_final: 0.8710 (p) outliers start: 10 outliers final: 5 residues processed: 143 average time/residue: 0.2311 time to fit residues: 52.4280 Evaluate side-chains 128 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN D 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15199 Z= 0.230 Angle : 0.561 10.325 20657 Z= 0.282 Chirality : 0.043 0.342 2387 Planarity : 0.003 0.037 2536 Dihedral : 9.593 115.955 2453 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.07 % Allowed : 8.78 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.49 (0.21), residues: 1764 helix: 2.07 (0.21), residues: 590 sheet: -0.61 (0.24), residues: 460 loop : -0.42 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 241 HIS 0.004 0.001 HIS D 110 PHE 0.018 0.001 PHE C 293 TYR 0.017 0.001 TYR B 299 ARG 0.003 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.713 Fit side-chains REVERT: A 597 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 227 MET cc_start: 0.8063 (ppp) cc_final: 0.7451 (ppp) REVERT: C 49 MET cc_start: 0.8294 (ppp) cc_final: 0.7887 (ppp) REVERT: C 95 ASP cc_start: 0.8393 (p0) cc_final: 0.7911 (p0) REVERT: E 49 MET cc_start: 0.8255 (mmm) cc_final: 0.7783 (tmm) REVERT: E 185 GLN cc_start: 0.9028 (pm20) cc_final: 0.8556 (pm20) REVERT: E 278 VAL cc_start: 0.8594 (p) cc_final: 0.7591 (m) REVERT: D 229 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8339 (tp-100) REVERT: D 258 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: F 414 HIS cc_start: 0.8129 (m90) cc_final: 0.7717 (m90) outliers start: 17 outliers final: 7 residues processed: 144 average time/residue: 0.2212 time to fit residues: 50.9069 Evaluate side-chains 134 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 303 ASN E 65 GLN D 102 HIS D 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15199 Z= 0.469 Angle : 0.658 7.893 20657 Z= 0.331 Chirality : 0.046 0.364 2387 Planarity : 0.004 0.038 2536 Dihedral : 9.126 120.159 2453 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.90 % Allowed : 10.04 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.23 (0.20), residues: 1764 helix: 1.88 (0.21), residues: 592 sheet: -0.79 (0.23), residues: 462 loop : -0.57 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 237 HIS 0.006 0.001 HIS E 107 PHE 0.018 0.002 PHE A 672 TYR 0.019 0.002 TYR C 157 ARG 0.005 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.614 Fit side-chains REVERT: A 597 GLN cc_start: 0.8618 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 55 MET cc_start: 0.9046 (mmp) cc_final: 0.8680 (mmp) REVERT: B 227 MET cc_start: 0.8111 (ppp) cc_final: 0.7492 (ppp) REVERT: C 49 MET cc_start: 0.8312 (ppp) cc_final: 0.7886 (ppp) REVERT: C 95 ASP cc_start: 0.8392 (p0) cc_final: 0.7973 (p0) REVERT: E 49 MET cc_start: 0.8263 (mmm) cc_final: 0.7773 (tmm) REVERT: E 185 GLN cc_start: 0.9046 (pm20) cc_final: 0.8724 (pm20) REVERT: F 5 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8243 (mm-40) REVERT: F 414 HIS cc_start: 0.8219 (m90) cc_final: 0.7846 (m90) REVERT: F 456 THR cc_start: 0.9356 (m) cc_final: 0.8968 (p) outliers start: 30 outliers final: 16 residues processed: 145 average time/residue: 0.2142 time to fit residues: 50.1017 Evaluate side-chains 137 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15199 Z= 0.188 Angle : 0.554 8.367 20657 Z= 0.279 Chirality : 0.043 0.362 2387 Planarity : 0.003 0.039 2536 Dihedral : 8.374 114.396 2453 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.20 % Allowed : 11.12 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.54 (0.21), residues: 1764 helix: 2.19 (0.22), residues: 590 sheet: -0.58 (0.24), residues: 448 loop : -0.48 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 237 HIS 0.004 0.001 HIS D 110 PHE 0.011 0.001 PHE D 258 TYR 0.017 0.001 TYR B 299 ARG 0.004 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.802 Fit side-chains REVERT: A 597 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 662 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7783 (t80) REVERT: B 55 MET cc_start: 0.9075 (mmp) cc_final: 0.8382 (mmp) REVERT: B 227 MET cc_start: 0.8046 (ppp) cc_final: 0.7409 (ppp) REVERT: C 49 MET cc_start: 0.8344 (ppp) cc_final: 0.8027 (ppp) REVERT: C 95 ASP cc_start: 0.8392 (p0) cc_final: 0.7875 (p0) REVERT: C 284 TYR cc_start: 0.8513 (t80) cc_final: 0.8185 (t80) REVERT: E 49 MET cc_start: 0.8285 (mmm) cc_final: 0.7810 (tmm) REVERT: E 185 GLN cc_start: 0.9007 (pm20) cc_final: 0.8792 (pm20) REVERT: D 148 MET cc_start: 0.8468 (mpp) cc_final: 0.8163 (mpp) REVERT: F 456 THR cc_start: 0.9360 (m) cc_final: 0.8977 (p) outliers start: 19 outliers final: 9 residues processed: 141 average time/residue: 0.2212 time to fit residues: 49.8657 Evaluate side-chains 139 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15199 Z= 0.328 Angle : 0.589 8.805 20657 Z= 0.296 Chirality : 0.044 0.363 2387 Planarity : 0.003 0.039 2536 Dihedral : 8.071 113.220 2453 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.58 % Allowed : 12.13 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.52 (0.21), residues: 1764 helix: 2.12 (0.21), residues: 592 sheet: -0.62 (0.24), residues: 455 loop : -0.42 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 237 HIS 0.004 0.001 HIS E 107 PHE 0.014 0.001 PHE D 304 TYR 0.019 0.001 TYR B 299 ARG 0.003 0.000 ARG D 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.860 Fit side-chains REVERT: A 597 GLN cc_start: 0.8608 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 662 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7807 (t80) REVERT: B 224 GLN cc_start: 0.8720 (tp40) cc_final: 0.8240 (tm-30) REVERT: B 227 MET cc_start: 0.8047 (ppp) cc_final: 0.7389 (ppp) REVERT: C 49 MET cc_start: 0.8354 (ppp) cc_final: 0.8022 (ppp) REVERT: C 95 ASP cc_start: 0.8392 (p0) cc_final: 0.7951 (p0) REVERT: E 49 MET cc_start: 0.8270 (mmm) cc_final: 0.7789 (tmm) REVERT: E 190 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: D 148 MET cc_start: 0.8501 (mpp) cc_final: 0.8203 (mpp) REVERT: F 456 THR cc_start: 0.9399 (m) cc_final: 0.9020 (p) outliers start: 25 outliers final: 17 residues processed: 142 average time/residue: 0.2372 time to fit residues: 53.5567 Evaluate side-chains 145 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 169 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15199 Z= 0.291 Angle : 0.585 9.529 20657 Z= 0.294 Chirality : 0.044 0.360 2387 Planarity : 0.003 0.039 2536 Dihedral : 7.569 110.261 2453 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.90 % Allowed : 12.51 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.57 (0.21), residues: 1764 helix: 2.17 (0.21), residues: 592 sheet: -0.60 (0.24), residues: 455 loop : -0.40 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 237 HIS 0.003 0.001 HIS D 110 PHE 0.012 0.001 PHE D 304 TYR 0.018 0.001 TYR B 299 ARG 0.004 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.619 Fit side-chains REVERT: A 141 MET cc_start: 0.7949 (mmm) cc_final: 0.7568 (mtp) REVERT: A 597 GLN cc_start: 0.8592 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 634 MET cc_start: 0.8948 (mmm) cc_final: 0.8719 (mmm) REVERT: A 662 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7686 (t80) REVERT: B 227 MET cc_start: 0.8047 (ppp) cc_final: 0.7387 (ppp) REVERT: C 49 MET cc_start: 0.8344 (ppp) cc_final: 0.8004 (ppp) REVERT: C 95 ASP cc_start: 0.8388 (p0) cc_final: 0.7986 (p0) REVERT: C 284 TYR cc_start: 0.8573 (t80) cc_final: 0.8254 (t80) REVERT: E 49 MET cc_start: 0.8285 (mmm) cc_final: 0.7805 (tmm) REVERT: E 190 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: D 148 MET cc_start: 0.8495 (mpp) cc_final: 0.8225 (mpp) REVERT: F 456 THR cc_start: 0.9423 (m) cc_final: 0.9051 (p) REVERT: F 483 CYS cc_start: 0.3391 (p) cc_final: 0.2840 (p) outliers start: 30 outliers final: 21 residues processed: 147 average time/residue: 0.2168 time to fit residues: 51.0844 Evaluate side-chains 153 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 433 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15199 Z= 0.171 Angle : 0.551 10.540 20657 Z= 0.276 Chirality : 0.043 0.355 2387 Planarity : 0.003 0.041 2536 Dihedral : 7.013 104.259 2453 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 1.45 % Allowed : 13.01 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.76 (0.21), residues: 1764 helix: 2.38 (0.22), residues: 583 sheet: -0.48 (0.24), residues: 450 loop : -0.31 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 237 HIS 0.003 0.000 HIS D 110 PHE 0.012 0.001 PHE D 157 TYR 0.016 0.001 TYR B 299 ARG 0.003 0.000 ARG E 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.825 Fit side-chains REVERT: A 141 MET cc_start: 0.7825 (mmm) cc_final: 0.7445 (mtp) REVERT: A 597 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 662 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 49 MET cc_start: 0.8377 (ppp) cc_final: 0.8053 (ppp) REVERT: C 95 ASP cc_start: 0.8393 (p0) cc_final: 0.7937 (p0) REVERT: C 284 TYR cc_start: 0.8494 (t80) cc_final: 0.8229 (t80) REVERT: E 49 MET cc_start: 0.8295 (mmm) cc_final: 0.7802 (tmm) REVERT: E 55 MET cc_start: 0.8617 (mmm) cc_final: 0.8136 (mmm) REVERT: E 95 ASP cc_start: 0.8233 (p0) cc_final: 0.7813 (p0) REVERT: F 1 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 421 MET cc_start: 0.8408 (mtt) cc_final: 0.8206 (mtt) REVERT: F 456 THR cc_start: 0.9436 (m) cc_final: 0.9086 (p) REVERT: F 467 TYR cc_start: 0.8383 (m-80) cc_final: 0.7908 (m-80) outliers start: 23 outliers final: 16 residues processed: 148 average time/residue: 0.2165 time to fit residues: 51.2006 Evaluate side-chains 144 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 149 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15199 Z= 0.187 Angle : 0.561 13.195 20657 Z= 0.279 Chirality : 0.042 0.359 2387 Planarity : 0.003 0.041 2536 Dihedral : 6.690 101.142 2453 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 1.45 % Allowed : 13.14 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.84 (0.21), residues: 1764 helix: 2.43 (0.22), residues: 584 sheet: -0.44 (0.24), residues: 455 loop : -0.26 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 237 HIS 0.003 0.001 HIS D 110 PHE 0.011 0.001 PHE D 157 TYR 0.017 0.001 TYR B 299 ARG 0.003 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.727 Fit side-chains REVERT: A 141 MET cc_start: 0.7824 (mmm) cc_final: 0.7439 (mtp) REVERT: A 581 MET cc_start: 0.8217 (mmm) cc_final: 0.7559 (mmm) REVERT: A 597 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 662 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7699 (t80) REVERT: C 49 MET cc_start: 0.8389 (ppp) cc_final: 0.8040 (ppp) REVERT: C 95 ASP cc_start: 0.8388 (p0) cc_final: 0.7972 (p0) REVERT: E 9 MET cc_start: 0.8510 (tpp) cc_final: 0.8239 (tpp) REVERT: E 49 MET cc_start: 0.8312 (mmm) cc_final: 0.7826 (tmm) REVERT: E 95 ASP cc_start: 0.8214 (p0) cc_final: 0.7798 (p0) REVERT: D 148 MET cc_start: 0.8371 (mpp) cc_final: 0.8063 (mpp) REVERT: F 1 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7539 (tm-30) REVERT: F 456 THR cc_start: 0.9444 (m) cc_final: 0.9100 (p) REVERT: F 467 TYR cc_start: 0.8405 (m-80) cc_final: 0.7995 (m-80) REVERT: F 504 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8269 (mm-40) outliers start: 23 outliers final: 19 residues processed: 146 average time/residue: 0.2231 time to fit residues: 52.3545 Evaluate side-chains 150 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 433 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15199 Z= 0.172 Angle : 0.560 11.483 20657 Z= 0.278 Chirality : 0.043 0.355 2387 Planarity : 0.003 0.041 2536 Dihedral : 6.390 96.811 2453 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 1.45 % Allowed : 12.89 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.91 (0.21), residues: 1764 helix: 2.45 (0.22), residues: 583 sheet: -0.31 (0.24), residues: 436 loop : -0.25 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 237 HIS 0.005 0.001 HIS B 267 PHE 0.012 0.001 PHE D 157 TYR 0.017 0.001 TYR B 299 ARG 0.002 0.000 ARG A 642 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.851 Fit side-chains REVERT: A 141 MET cc_start: 0.7781 (mmm) cc_final: 0.7403 (mtp) REVERT: A 581 MET cc_start: 0.8178 (mmm) cc_final: 0.7546 (mmm) REVERT: A 597 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 634 MET cc_start: 0.9160 (mmm) cc_final: 0.8614 (mmm) REVERT: A 662 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 237 TRP cc_start: 0.8833 (m-10) cc_final: 0.8487 (m-10) REVERT: C 49 MET cc_start: 0.8413 (ppp) cc_final: 0.8038 (ppp) REVERT: C 95 ASP cc_start: 0.8392 (p0) cc_final: 0.8017 (p0) REVERT: E 9 MET cc_start: 0.8519 (tpp) cc_final: 0.8243 (tpp) REVERT: E 49 MET cc_start: 0.8314 (mmm) cc_final: 0.7858 (tmm) REVERT: E 95 ASP cc_start: 0.8149 (p0) cc_final: 0.7746 (p0) REVERT: D 148 MET cc_start: 0.8339 (mpp) cc_final: 0.8066 (mpp) REVERT: F 1 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7593 (tm-30) REVERT: F 409 CYS cc_start: 0.4218 (t) cc_final: 0.3738 (t) REVERT: F 446 SER cc_start: 0.8955 (t) cc_final: 0.8514 (t) REVERT: F 456 THR cc_start: 0.9464 (m) cc_final: 0.9133 (p) REVERT: F 467 TYR cc_start: 0.8394 (m-80) cc_final: 0.7980 (m-80) REVERT: F 504 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8274 (mm-40) outliers start: 23 outliers final: 21 residues processed: 148 average time/residue: 0.2240 time to fit residues: 53.0116 Evaluate side-chains 153 residues out of total 1583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053301 restraints weight = 48121.495| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.46 r_work: 0.2837 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15199 Z= 0.211 Angle : 0.567 9.580 20657 Z= 0.282 Chirality : 0.043 0.360 2387 Planarity : 0.003 0.041 2536 Dihedral : 6.217 93.294 2453 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 1.39 % Allowed : 13.39 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.91 (0.21), residues: 1764 helix: 2.42 (0.22), residues: 585 sheet: -0.31 (0.24), residues: 442 loop : -0.22 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 237 HIS 0.003 0.001 HIS D 110 PHE 0.011 0.001 PHE D 157 TYR 0.018 0.001 TYR B 299 ARG 0.002 0.000 ARG E 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.64 seconds wall clock time: 55 minutes 27.25 seconds (3327.25 seconds total)