Starting phenix.real_space_refine on Thu Sep 18 10:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o52_70121/09_2025/9o52_70121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o52_70121/09_2025/9o52_70121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o52_70121/09_2025/9o52_70121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o52_70121/09_2025/9o52_70121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o52_70121/09_2025/9o52_70121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o52_70121/09_2025/9o52_70121.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 K 4 8.98 5 S 130 5.16 5 C 10332 2.51 5 N 2736 2.21 5 O 2967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16185 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1048 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 93 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.02, per 1000 atoms: 0.25 Number of scatterers: 16185 At special positions: 0 Unit cell: (120.835, 120.835, 103.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 16 19.99 K 4 19.00 S 130 16.00 O 2967 8.00 N 2736 7.00 C 10332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 332 " - pdb=" SG CYS D 370 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 590.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 4 sheets defined 78.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 118 through 157 removed outlier: 3.552A pdb=" N ARG A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 200 removed outlier: 3.870A pdb=" N LEU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 210 through 225 Processing helix chain 'A' and resid 259 through 265 Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.036A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 309 through 333 removed outlier: 3.571A pdb=" N LEU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.593A pdb=" N SER A 353 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 354 " --> pdb=" O TRP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.577A pdb=" N GLY A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 439 removed outlier: 3.822A pdb=" N HIS A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 477 Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'B' and resid 119 through 157 removed outlier: 3.722A pdb=" N TRP B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 200 removed outlier: 4.005A pdb=" N CYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.591A pdb=" N MET B 209 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.585A pdb=" N PHE B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 265 Processing helix chain 'B' and resid 266 through 276 removed outlier: 4.117A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.262A pdb=" N THR B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.517A pdb=" N ASN B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 309 through 334 removed outlier: 3.586A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.652A pdb=" N TRP B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 353 " --> pdb=" O MET B 349 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 396 removed outlier: 3.589A pdb=" N LEU B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 439 removed outlier: 3.953A pdb=" N HIS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 477 Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'C' and resid 119 through 159 removed outlier: 3.744A pdb=" N TRP C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 170 through 200 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 210 through 225 Processing helix chain 'C' and resid 253 through 257 removed outlier: 3.679A pdb=" N ILE C 256 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 265 Processing helix chain 'C' and resid 266 through 276 removed outlier: 4.009A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.578A pdb=" N THR C 281 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.633A pdb=" N VAL C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 334 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 370 through 397 removed outlier: 3.609A pdb=" N GLY C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 439 Processing helix chain 'C' and resid 441 through 477 Processing helix chain 'C' and resid 477 through 490 Processing helix chain 'D' and resid 119 through 159 removed outlier: 3.621A pdb=" N ARG D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 170 through 200 removed outlier: 3.518A pdb=" N ILE D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.615A pdb=" N PHE D 215 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.745A pdb=" N ILE D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 276 removed outlier: 4.108A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 309 through 333 removed outlier: 3.582A pdb=" N LEU D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.608A pdb=" N TRP D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 397 removed outlier: 3.651A pdb=" N GLY D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 439 removed outlier: 3.805A pdb=" N VAL D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 477 Processing helix chain 'D' and resid 478 through 490 Processing helix chain 'E' and resid 6 through 21 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 81 through 94 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 6 through 21 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 81 through 94 removed outlier: 3.515A pdb=" N GLU H 85 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 120 through 130 Processing helix chain 'H' and resid 138 through 147 Processing helix chain 'I' and resid 8 through 17 removed outlier: 3.533A pdb=" N GLN I 16 " --> pdb=" O ALA I 12 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 240 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 240 Processing sheet with id=AA3, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AA4, first strand: chain 'D' and resid 234 through 240 1195 hydrogen bonds defined for protein. 3489 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: 2.54 Time building geometry restraints manager: 1.68 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: 5278 1.34 - 1.46: 3397 1.46 - 1.58: 7556 1.58 - 1.69: 0 1.69 - 1.81: 226 Bond restraints: 16457 Sorted by residual: bond pdb=" N GLY B 231 " pdb=" CA GLY B 231 " ideal model delta sigma weight residual 1.449 1.478 -0.029 1.00e-02 1.00e+04 8.50e+00 bond pdb=" N VAL D 198 " pdb=" CA VAL D 198 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 7.98e+00 bond pdb=" N ASP D 203 " pdb=" CA ASP D 203 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 6.99e+00 bond pdb=" N GLN C 339 " pdb=" CA GLN C 339 " ideal model delta sigma weight residual 1.458 1.487 -0.028 1.08e-02 8.57e+03 6.95e+00 bond pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.35e-02 5.49e+03 6.90e+00 ... (remaining 16452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 21809 1.40 - 2.80: 375 2.80 - 4.21: 58 4.21 - 5.61: 9 5.61 - 7.01: 3 Bond angle restraints: 22254 Sorted by residual: angle pdb=" N ILE C 354 " pdb=" CA ILE C 354 " pdb=" C ILE C 354 " ideal model delta sigma weight residual 112.90 107.86 5.04 9.60e-01 1.09e+00 2.76e+01 angle pdb=" CA GLY B 231 " pdb=" C GLY B 231 " pdb=" O GLY B 231 " ideal model delta sigma weight residual 122.33 118.19 4.14 8.10e-01 1.52e+00 2.61e+01 angle pdb=" CA GLY B 231 " pdb=" C GLY B 231 " pdb=" N ASN B 232 " ideal model delta sigma weight residual 114.23 117.53 -3.30 8.80e-01 1.29e+00 1.40e+01 angle pdb=" N ASP D 203 " pdb=" CA ASP D 203 " pdb=" C ASP D 203 " ideal model delta sigma weight residual 114.31 109.81 4.50 1.29e+00 6.01e-01 1.22e+01 angle pdb=" N VAL D 198 " pdb=" CA VAL D 198 " pdb=" C VAL D 198 " ideal model delta sigma weight residual 110.82 107.51 3.31 9.70e-01 1.06e+00 1.16e+01 ... (remaining 22249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8808 16.53 - 33.05: 846 33.05 - 49.58: 165 49.58 - 66.11: 26 66.11 - 82.63: 2 Dihedral angle restraints: 9847 sinusoidal: 3844 harmonic: 6003 Sorted by residual: dihedral pdb=" CD ARG I 13 " pdb=" NE ARG I 13 " pdb=" CZ ARG I 13 " pdb=" NH1 ARG I 13 " ideal model delta sinusoidal sigma weight residual 0.00 -46.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS A 332 " pdb=" SG CYS A 332 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 54.80 38.20 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CB CYS B 332 " pdb=" SG CYS B 332 " pdb=" SG CYS B 370 " pdb=" CB CYS B 370 " ideal model delta sinusoidal sigma weight residual 93.00 59.12 33.88 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 9844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1825 0.037 - 0.073: 656 0.073 - 0.110: 80 0.110 - 0.146: 18 0.146 - 0.183: 3 Chirality restraints: 2582 Sorted by residual: chirality pdb=" CA VAL D 198 " pdb=" N VAL D 198 " pdb=" C VAL D 198 " pdb=" CB VAL D 198 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA ILE C 352 " pdb=" N ILE C 352 " pdb=" C ILE C 352 " pdb=" CB ILE C 352 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN B 232 " pdb=" N ASN B 232 " pdb=" C ASN B 232 " pdb=" CB ASN B 232 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2579 not shown) Planarity restraints: 2803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 13 " -0.790 9.50e-02 1.11e+02 3.54e-01 7.64e+01 pdb=" NE ARG I 13 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG I 13 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG I 13 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 13 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 123 " 0.131 9.50e-02 1.11e+02 5.88e-02 2.15e+00 pdb=" NE ARG A 123 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 123 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 123 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 123 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 260 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 261 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.019 5.00e-02 4.00e+02 ... (remaining 2800 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 4968 2.82 - 3.40: 18123 3.40 - 3.98: 29971 3.98 - 4.56: 44501 4.56 - 5.14: 62686 Nonbonded interactions: 160249 Sorted by model distance: nonbonded pdb=" OD1 ASP F 134 " pdb="CA CA F 504 " model vdw 2.243 2.510 nonbonded pdb=" OE1 GLU H 105 " pdb="CA CA H 503 " model vdw 2.289 2.510 nonbonded pdb=" OD1 ASP H 57 " pdb="CA CA H 502 " model vdw 2.292 2.510 nonbonded pdb=" OE1 GLU G 105 " pdb="CA CA G 503 " model vdw 2.296 2.510 nonbonded pdb=" OE1 GLU G 32 " pdb="CA CA G 501 " model vdw 2.299 2.510 ... (remaining 160244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 118 through 490) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 118 through 490) } ncs_group { reference = (chain 'E' and (resid 4 through 127 or (resid 128 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 504)) selection = chain 'F' selection = (chain 'G' and (resid 4 through 127 or (resid 128 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 504)) selection = (chain 'H' and (resid 4 through 127 or (resid 128 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 504)) } 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.380 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.003 0.035 16461 Z= 0.169 Angle : 0.465 7.012 22262 Z= 0.297 Chirality : 0.036 0.183 2582 Planarity : 0.007 0.354 2803 Dihedral : 13.096 82.634 5939 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.18), residues: 2030 helix: 0.00 (0.13), residues: 1512 sheet: 0.04 (0.62), residues: 64 loop : 0.08 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 13 TYR 0.017 0.001 TYR B 245 PHE 0.009 0.001 PHE A 345 TRP 0.006 0.001 TRP A 350 HIS 0.002 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00310 (16457) covalent geometry : angle 0.46511 (22254) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.40866 ( 8) hydrogen bonds : bond 0.20969 ( 1195) hydrogen bonds : angle 6.95644 ( 3489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7702 (tp30) REVERT: A 204 ASP cc_start: 0.7644 (t70) cc_final: 0.7320 (t70) REVERT: A 340 ASP cc_start: 0.7937 (t70) cc_final: 0.7692 (t70) REVERT: A 377 LEU cc_start: 0.8105 (tp) cc_final: 0.7576 (mp) REVERT: A 395 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7634 (mtm-85) REVERT: A 404 LYS cc_start: 0.8184 (mttt) cc_final: 0.7567 (mtpp) REVERT: A 411 MET cc_start: 0.8224 (mmt) cc_final: 0.7459 (mtm) REVERT: A 447 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.7076 (tpt170) REVERT: A 465 LYS cc_start: 0.8572 (ptmt) cc_final: 0.8227 (ptpt) REVERT: B 132 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7670 (ttpp) REVERT: B 165 LEU cc_start: 0.8116 (tp) cc_final: 0.7641 (tt) REVERT: B 236 THR cc_start: 0.9012 (m) cc_final: 0.8779 (t) REVERT: B 333 GLU cc_start: 0.8001 (tp30) cc_final: 0.7748 (mm-30) REVERT: B 432 MET cc_start: 0.7798 (tpp) cc_final: 0.7428 (mtm) REVERT: B 447 ARG cc_start: 0.7683 (ttp-110) cc_final: 0.7373 (ttp-110) REVERT: B 461 GLN cc_start: 0.7758 (mm110) cc_final: 0.7358 (mt0) REVERT: B 467 ARG cc_start: 0.7287 (ttt90) cc_final: 0.6816 (ttp80) REVERT: B 468 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7729 (mttt) REVERT: B 470 ARG cc_start: 0.7559 (mmp80) cc_final: 0.7256 (mmp80) REVERT: C 164 SER cc_start: 0.8547 (t) cc_final: 0.8014 (p) REVERT: C 210 THR cc_start: 0.8378 (p) cc_final: 0.7935 (t) REVERT: C 306 MET cc_start: 0.8526 (mmm) cc_final: 0.8226 (mmm) REVERT: C 349 MET cc_start: 0.8854 (ttp) cc_final: 0.8632 (ttt) REVERT: C 377 LEU cc_start: 0.7879 (tp) cc_final: 0.7635 (mt) REVERT: C 403 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 411 MET cc_start: 0.8026 (mmt) cc_final: 0.7374 (mtm) REVERT: C 420 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7330 (mmmt) REVERT: C 425 ARG cc_start: 0.6644 (mtm-85) cc_final: 0.6218 (mmt180) REVERT: C 447 ARG cc_start: 0.7305 (ttp-110) cc_final: 0.6705 (tpt170) REVERT: C 461 GLN cc_start: 0.7847 (mm110) cc_final: 0.7574 (mt0) REVERT: C 467 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7419 (ttt-90) REVERT: C 470 ARG cc_start: 0.6864 (mtm180) cc_final: 0.6439 (mmm-85) REVERT: D 168 LEU cc_start: 0.8427 (tp) cc_final: 0.8223 (tp) REVERT: D 293 LYS cc_start: 0.7590 (mmtt) cc_final: 0.6630 (mppt) REVERT: D 299 ARG cc_start: 0.7394 (mtt180) cc_final: 0.6357 (mtp85) REVERT: D 377 LEU cc_start: 0.8136 (tp) cc_final: 0.7741 (mp) REVERT: D 447 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.7033 (tpt170) REVERT: D 451 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7479 (mtpt) REVERT: D 468 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7000 (mttt) REVERT: E 39 SER cc_start: 0.8438 (t) cc_final: 0.7883 (p) REVERT: F 94 ASP cc_start: 0.5025 (t70) cc_final: 0.4332 (p0) REVERT: G 39 SER cc_start: 0.8247 (t) cc_final: 0.7995 (p) REVERT: G 46 GLU cc_start: 0.7704 (tp30) cc_final: 0.7406 (mm-30) REVERT: G 110 MET cc_start: 0.7024 (mmt) cc_final: 0.5541 (ppp) REVERT: H 14 LYS cc_start: 0.7485 (mttt) cc_final: 0.6652 (tptt) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1541 time to fit residues: 91.9565 Evaluate side-chains 326 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN B 232 ASN C 448 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132687 restraints weight = 16655.977| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.72 r_work: 0.3317 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16461 Z= 0.116 Angle : 0.450 9.418 22262 Z= 0.242 Chirality : 0.037 0.180 2582 Planarity : 0.004 0.032 2803 Dihedral : 3.523 16.172 2225 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.70 % Allowed : 8.74 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 2030 helix: 1.52 (0.13), residues: 1539 sheet: 0.19 (0.63), residues: 64 loop : 0.20 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.015 0.001 TYR B 245 PHE 0.014 0.001 PHE A 128 TRP 0.009 0.001 TRP B 350 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00239 (16457) covalent geometry : angle 0.44997 (22254) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.50497 ( 8) hydrogen bonds : bond 0.04389 ( 1195) hydrogen bonds : angle 3.57628 ( 3489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 332 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7730 (t70) cc_final: 0.7465 (t70) REVERT: A 377 LEU cc_start: 0.8353 (tp) cc_final: 0.7975 (mp) REVERT: A 404 LYS cc_start: 0.8432 (mttt) cc_final: 0.7936 (mtpp) REVERT: A 411 MET cc_start: 0.8567 (mmt) cc_final: 0.7952 (mtm) REVERT: A 447 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.7218 (tpt170) REVERT: A 465 LYS cc_start: 0.8561 (ptmt) cc_final: 0.8288 (ptpt) REVERT: A 483 HIS cc_start: 0.7463 (m90) cc_final: 0.7179 (m170) REVERT: B 165 LEU cc_start: 0.8077 (tp) cc_final: 0.7573 (tt) REVERT: B 250 THR cc_start: 0.9041 (t) cc_final: 0.8650 (p) REVERT: B 396 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7824 (mtpt) REVERT: B 461 GLN cc_start: 0.7958 (mm110) cc_final: 0.7685 (mt0) REVERT: B 467 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7107 (ttp80) REVERT: B 468 LYS cc_start: 0.8253 (ttmm) cc_final: 0.8028 (mttt) REVERT: B 470 ARG cc_start: 0.7694 (mmp80) cc_final: 0.7382 (mmp80) REVERT: C 166 TYR cc_start: 0.8565 (m-80) cc_final: 0.8274 (m-80) REVERT: C 167 SER cc_start: 0.9075 (t) cc_final: 0.8858 (m) REVERT: C 303 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7759 (mtpt) REVERT: C 306 MET cc_start: 0.8849 (mmm) cc_final: 0.8631 (mmm) REVERT: C 411 MET cc_start: 0.8437 (mmt) cc_final: 0.7924 (mtm) REVERT: C 420 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7696 (mmmt) REVERT: C 425 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6448 (mmp-170) REVERT: C 447 ARG cc_start: 0.6910 (ttp-110) cc_final: 0.6614 (tpt170) REVERT: C 467 ARG cc_start: 0.7949 (ttt90) cc_final: 0.7740 (ttt-90) REVERT: D 293 LYS cc_start: 0.7803 (mmtt) cc_final: 0.6984 (mppt) REVERT: D 340 ASP cc_start: 0.7960 (t70) cc_final: 0.7746 (t70) REVERT: D 377 LEU cc_start: 0.8355 (tp) cc_final: 0.8129 (mp) REVERT: D 447 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.7019 (tpt170) REVERT: D 451 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7893 (mtpt) REVERT: D 468 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7300 (mttt) REVERT: E 39 SER cc_start: 0.8600 (t) cc_final: 0.8155 (p) REVERT: E 140 GLU cc_start: 0.8118 (pm20) cc_final: 0.7561 (mp0) REVERT: F 94 ASP cc_start: 0.5675 (t70) cc_final: 0.4740 (p0) REVERT: G 39 SER cc_start: 0.8559 (t) cc_final: 0.8327 (p) REVERT: G 46 GLU cc_start: 0.7874 (tp30) cc_final: 0.7589 (mm-30) REVERT: G 51 ASP cc_start: 0.7741 (t0) cc_final: 0.7479 (t0) REVERT: G 73 MET cc_start: 0.8250 (mmm) cc_final: 0.8031 (mmm) REVERT: G 110 MET cc_start: 0.7002 (mmt) cc_final: 0.5652 (ppp) REVERT: H 14 LYS cc_start: 0.7818 (mttt) cc_final: 0.6984 (tptt) REVERT: H 73 MET cc_start: 0.8138 (mmp) cc_final: 0.7748 (mmp) outliers start: 12 outliers final: 6 residues processed: 340 average time/residue: 0.1583 time to fit residues: 76.3750 Evaluate side-chains 302 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 296 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 137 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 83 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 GLN C 461 GLN C 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.162916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119497 restraints weight = 17085.604| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.86 r_work: 0.3205 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16461 Z= 0.150 Angle : 0.460 11.299 22262 Z= 0.243 Chirality : 0.038 0.175 2582 Planarity : 0.003 0.035 2803 Dihedral : 3.525 18.286 2225 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.88 % Allowed : 11.61 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.19), residues: 2030 helix: 2.00 (0.13), residues: 1538 sheet: 0.48 (0.68), residues: 64 loop : 0.29 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.017 0.001 TYR D 245 PHE 0.012 0.001 PHE A 356 TRP 0.008 0.001 TRP D 350 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00350 (16457) covalent geometry : angle 0.45961 (22254) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.32046 ( 8) hydrogen bonds : bond 0.04211 ( 1195) hydrogen bonds : angle 3.36221 ( 3489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 297 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7881 (t70) cc_final: 0.7669 (t70) REVERT: A 222 LEU cc_start: 0.8443 (tp) cc_final: 0.8220 (tp) REVERT: A 377 LEU cc_start: 0.8359 (tp) cc_final: 0.7985 (mp) REVERT: A 404 LYS cc_start: 0.8455 (mttt) cc_final: 0.7920 (mtpp) REVERT: A 411 MET cc_start: 0.8669 (mmt) cc_final: 0.7976 (mtm) REVERT: A 447 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.7120 (tpt170) REVERT: A 465 LYS cc_start: 0.8467 (ptmt) cc_final: 0.8255 (ptpt) REVERT: B 165 LEU cc_start: 0.8149 (tp) cc_final: 0.7639 (tt) REVERT: B 396 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7985 (mtpt) REVERT: B 447 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7719 (ttp-110) REVERT: B 461 GLN cc_start: 0.7931 (mm110) cc_final: 0.7651 (mt0) REVERT: B 467 ARG cc_start: 0.7596 (ttt90) cc_final: 0.7050 (ttp80) REVERT: B 468 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8002 (mttt) REVERT: B 470 ARG cc_start: 0.7574 (mmp80) cc_final: 0.7345 (mmp80) REVERT: C 167 SER cc_start: 0.9091 (t) cc_final: 0.8886 (m) REVERT: C 411 MET cc_start: 0.8422 (mmt) cc_final: 0.7937 (mtm) REVERT: C 420 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7628 (mmmt) REVERT: C 425 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6223 (mmp-170) REVERT: C 447 ARG cc_start: 0.6901 (ttp-110) cc_final: 0.6491 (tpt170) REVERT: C 467 ARG cc_start: 0.7912 (ttt90) cc_final: 0.7685 (ttt-90) REVERT: D 293 LYS cc_start: 0.7796 (mmtt) cc_final: 0.6903 (mppt) REVERT: D 377 LEU cc_start: 0.8345 (tp) cc_final: 0.8139 (mp) REVERT: D 447 ARG cc_start: 0.7481 (ttp-110) cc_final: 0.6843 (tpt170) REVERT: D 451 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7669 (mtpt) REVERT: D 468 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7179 (mttt) REVERT: E 39 SER cc_start: 0.8683 (t) cc_final: 0.8338 (p) REVERT: F 94 ASP cc_start: 0.5408 (t70) cc_final: 0.4639 (p0) REVERT: G 39 SER cc_start: 0.8571 (t) cc_final: 0.8301 (p) REVERT: G 46 GLU cc_start: 0.7788 (tp30) cc_final: 0.7559 (mm-30) REVERT: G 110 MET cc_start: 0.6988 (mmt) cc_final: 0.5611 (ppp) REVERT: H 14 LYS cc_start: 0.7752 (mttt) cc_final: 0.6894 (tptt) REVERT: H 73 MET cc_start: 0.8065 (mmp) cc_final: 0.7705 (mmp) outliers start: 15 outliers final: 12 residues processed: 305 average time/residue: 0.1525 time to fit residues: 65.7312 Evaluate side-chains 294 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 282 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain G residue 52 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 191 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS B 448 HIS C 461 GLN C 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.161820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118752 restraints weight = 16936.019| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.81 r_work: 0.3181 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16461 Z= 0.195 Angle : 0.500 12.252 22262 Z= 0.263 Chirality : 0.040 0.179 2582 Planarity : 0.004 0.037 2803 Dihedral : 3.712 20.253 2225 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.52 % Allowed : 12.55 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.19), residues: 2030 helix: 1.98 (0.13), residues: 1563 sheet: 0.31 (0.65), residues: 64 loop : 0.59 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.018 0.001 TYR B 245 PHE 0.015 0.001 PHE A 356 TRP 0.009 0.001 TRP B 350 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00467 (16457) covalent geometry : angle 0.50038 (22254) SS BOND : bond 0.00403 ( 4) SS BOND : angle 0.21603 ( 8) hydrogen bonds : bond 0.04442 ( 1195) hydrogen bonds : angle 3.36270 ( 3489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8424 (tp) cc_final: 0.8211 (tp) REVERT: A 377 LEU cc_start: 0.8331 (tp) cc_final: 0.7944 (mp) REVERT: A 404 LYS cc_start: 0.8489 (mttt) cc_final: 0.8226 (mtmt) REVERT: A 411 MET cc_start: 0.8641 (mmt) cc_final: 0.7960 (mtm) REVERT: A 447 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.7063 (tpt170) REVERT: A 465 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8185 (ptpt) REVERT: B 165 LEU cc_start: 0.8203 (tp) cc_final: 0.7676 (tt) REVERT: B 461 GLN cc_start: 0.7922 (mm110) cc_final: 0.7557 (mt0) REVERT: B 467 ARG cc_start: 0.7542 (ttt90) cc_final: 0.6971 (ttp80) REVERT: B 468 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7946 (mttt) REVERT: B 470 ARG cc_start: 0.7533 (mmp80) cc_final: 0.7262 (mmp80) REVERT: C 167 SER cc_start: 0.9063 (t) cc_final: 0.8862 (m) REVERT: C 340 ASP cc_start: 0.7978 (t70) cc_final: 0.7564 (t0) REVERT: C 411 MET cc_start: 0.8353 (mmt) cc_final: 0.7868 (mtm) REVERT: C 420 LYS cc_start: 0.8109 (mmtp) cc_final: 0.7494 (mmmt) REVERT: C 425 ARG cc_start: 0.6737 (mtm-85) cc_final: 0.6129 (mmp-170) REVERT: C 447 ARG cc_start: 0.6855 (ttp-110) cc_final: 0.6396 (tpt170) REVERT: C 467 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7538 (ttt-90) REVERT: C 470 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6721 (mmm-85) REVERT: D 293 LYS cc_start: 0.7650 (mmtt) cc_final: 0.6744 (mppt) REVERT: D 377 LEU cc_start: 0.8308 (tp) cc_final: 0.8033 (mp) REVERT: D 447 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.6764 (tpt170) REVERT: D 451 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7607 (mtpt) REVERT: D 468 LYS cc_start: 0.7943 (ttmm) cc_final: 0.6888 (tptt) REVERT: E 39 SER cc_start: 0.8611 (t) cc_final: 0.8117 (p) REVERT: G 39 SER cc_start: 0.8591 (t) cc_final: 0.8314 (p) REVERT: G 110 MET cc_start: 0.6948 (mmt) cc_final: 0.5552 (ppp) REVERT: H 14 LYS cc_start: 0.7833 (mttt) cc_final: 0.6928 (tptt) outliers start: 26 outliers final: 23 residues processed: 307 average time/residue: 0.1476 time to fit residues: 65.2272 Evaluate side-chains 303 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 68 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 139 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 448 HIS B 448 HIS C 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.164510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121518 restraints weight = 16842.908| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.81 r_work: 0.3225 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16461 Z= 0.120 Angle : 0.438 12.414 22262 Z= 0.228 Chirality : 0.037 0.182 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.530 18.171 2225 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.00 % Allowed : 13.90 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.19), residues: 2030 helix: 2.30 (0.13), residues: 1564 sheet: 0.27 (0.64), residues: 64 loop : 0.77 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.019 0.001 TYR B 245 PHE 0.010 0.001 PHE A 356 TRP 0.009 0.001 TRP B 327 HIS 0.005 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00271 (16457) covalent geometry : angle 0.43761 (22254) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.31082 ( 8) hydrogen bonds : bond 0.03711 ( 1195) hydrogen bonds : angle 3.13206 ( 3489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 290 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8462 (tp) cc_final: 0.8251 (tp) REVERT: A 377 LEU cc_start: 0.8364 (tp) cc_final: 0.7995 (mp) REVERT: A 404 LYS cc_start: 0.8566 (mttt) cc_final: 0.7763 (mmmt) REVERT: A 411 MET cc_start: 0.8662 (mmt) cc_final: 0.7965 (mtm) REVERT: A 447 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7068 (tpt170) REVERT: A 465 LYS cc_start: 0.8396 (ptmt) cc_final: 0.8137 (ptpt) REVERT: B 165 LEU cc_start: 0.8182 (tp) cc_final: 0.7679 (tt) REVERT: B 461 GLN cc_start: 0.7981 (mm110) cc_final: 0.7658 (mt0) REVERT: B 467 ARG cc_start: 0.7604 (ttt90) cc_final: 0.7101 (ttp80) REVERT: B 468 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8037 (mttt) REVERT: B 470 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7190 (mmp80) REVERT: C 411 MET cc_start: 0.8485 (mmt) cc_final: 0.7975 (mtm) REVERT: C 420 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7628 (mmmt) REVERT: C 425 ARG cc_start: 0.6833 (mtm-85) cc_final: 0.6209 (mmp-170) REVERT: C 467 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7656 (ttt-90) REVERT: D 293 LYS cc_start: 0.7771 (mmtt) cc_final: 0.6940 (mppt) REVERT: D 377 LEU cc_start: 0.8326 (tp) cc_final: 0.8109 (mp) REVERT: D 447 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.6756 (tpt170) REVERT: D 451 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7712 (mtpt) REVERT: D 468 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7025 (tptt) REVERT: E 39 SER cc_start: 0.8729 (t) cc_final: 0.8316 (p) REVERT: G 39 SER cc_start: 0.8619 (t) cc_final: 0.8350 (p) REVERT: G 65 ASP cc_start: 0.7941 (p0) cc_final: 0.7087 (p0) REVERT: G 68 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: G 110 MET cc_start: 0.6930 (mmt) cc_final: 0.5634 (ppp) REVERT: H 14 LYS cc_start: 0.7748 (mttt) cc_final: 0.6880 (tptt) REVERT: H 73 MET cc_start: 0.8039 (mmp) cc_final: 0.7665 (mmp) outliers start: 17 outliers final: 14 residues processed: 302 average time/residue: 0.1304 time to fit residues: 57.2524 Evaluate side-chains 285 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 0.0010 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS B 448 HIS C 483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.165369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122575 restraints weight = 16788.934| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.80 r_work: 0.3214 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16461 Z= 0.108 Angle : 0.428 10.804 22262 Z= 0.223 Chirality : 0.036 0.201 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.425 17.371 2225 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.35 % Allowed : 14.31 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (0.19), residues: 2030 helix: 2.51 (0.13), residues: 1560 sheet: 0.33 (0.66), residues: 64 loop : 0.80 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.016 0.001 TYR B 245 PHE 0.009 0.001 PHE A 356 TRP 0.009 0.001 TRP B 327 HIS 0.005 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00236 (16457) covalent geometry : angle 0.42823 (22254) SS BOND : bond 0.00166 ( 4) SS BOND : angle 0.28232 ( 8) hydrogen bonds : bond 0.03493 ( 1195) hydrogen bonds : angle 3.06177 ( 3489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8804 (tmm) cc_final: 0.8439 (tmm) REVERT: A 222 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 377 LEU cc_start: 0.8357 (tp) cc_final: 0.7983 (mp) REVERT: A 404 LYS cc_start: 0.8550 (mttt) cc_final: 0.7751 (mmmt) REVERT: A 411 MET cc_start: 0.8642 (mmt) cc_final: 0.7936 (mtm) REVERT: A 447 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7042 (tpt170) REVERT: A 465 LYS cc_start: 0.8373 (ptmt) cc_final: 0.8080 (ptpt) REVERT: B 165 LEU cc_start: 0.8176 (tp) cc_final: 0.7675 (tt) REVERT: B 461 GLN cc_start: 0.7973 (mm110) cc_final: 0.7624 (mt0) REVERT: B 467 ARG cc_start: 0.7544 (ttt90) cc_final: 0.7051 (ttp80) REVERT: B 468 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8027 (mttt) REVERT: B 470 ARG cc_start: 0.7602 (mmp80) cc_final: 0.7169 (mmp80) REVERT: C 330 ARG cc_start: 0.8861 (ttt90) cc_final: 0.8601 (ttt90) REVERT: C 411 MET cc_start: 0.8474 (mmt) cc_final: 0.7925 (mtm) REVERT: C 420 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7613 (mmmt) REVERT: C 425 ARG cc_start: 0.6805 (mtm-85) cc_final: 0.6154 (mmp-170) REVERT: C 467 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7645 (ttt-90) REVERT: D 192 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7941 (mt-10) REVERT: D 293 LYS cc_start: 0.7811 (mmtt) cc_final: 0.6823 (mppt) REVERT: D 447 ARG cc_start: 0.7457 (ttp-110) cc_final: 0.6692 (tpt170) REVERT: D 468 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7038 (tptt) REVERT: E 35 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7959 (p) REVERT: E 39 SER cc_start: 0.8694 (t) cc_final: 0.8314 (p) REVERT: G 39 SER cc_start: 0.8661 (t) cc_final: 0.8394 (p) REVERT: G 110 MET cc_start: 0.6903 (mmt) cc_final: 0.5740 (ppp) REVERT: H 14 LYS cc_start: 0.7790 (mttt) cc_final: 0.6905 (tptt) REVERT: H 73 MET cc_start: 0.8025 (mmp) cc_final: 0.7666 (mmp) outliers start: 23 outliers final: 16 residues processed: 284 average time/residue: 0.1451 time to fit residues: 59.6651 Evaluate side-chains 275 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 68 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 61 optimal weight: 0.0270 chunk 153 optimal weight: 0.4980 chunk 155 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS B 448 HIS C 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.165890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123137 restraints weight = 16693.018| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.81 r_work: 0.3234 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16461 Z= 0.101 Angle : 0.425 12.710 22262 Z= 0.220 Chirality : 0.036 0.173 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.356 16.778 2225 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.35 % Allowed : 14.13 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.39 (0.19), residues: 2030 helix: 2.75 (0.13), residues: 1536 sheet: 0.43 (0.67), residues: 64 loop : 0.66 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 38 TYR 0.017 0.001 TYR B 245 PHE 0.009 0.001 PHE D 409 TRP 0.009 0.001 TRP B 327 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00218 (16457) covalent geometry : angle 0.42509 (22254) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.28130 ( 8) hydrogen bonds : bond 0.03327 ( 1195) hydrogen bonds : angle 2.97705 ( 3489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8812 (tmm) cc_final: 0.8472 (tmm) REVERT: A 179 ILE cc_start: 0.8637 (mm) cc_final: 0.8342 (mt) REVERT: A 222 LEU cc_start: 0.8421 (tp) cc_final: 0.8199 (tp) REVERT: A 377 LEU cc_start: 0.8371 (tp) cc_final: 0.8001 (mp) REVERT: A 411 MET cc_start: 0.8646 (mmt) cc_final: 0.7931 (mtm) REVERT: A 447 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7015 (tpt170) REVERT: B 165 LEU cc_start: 0.8133 (tp) cc_final: 0.7653 (tt) REVERT: B 461 GLN cc_start: 0.7914 (mm110) cc_final: 0.7543 (mt0) REVERT: B 467 ARG cc_start: 0.7561 (ttt90) cc_final: 0.7083 (ttp80) REVERT: B 468 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8037 (mttt) REVERT: B 470 ARG cc_start: 0.7549 (mmp80) cc_final: 0.7111 (mmp80) REVERT: C 330 ARG cc_start: 0.8832 (ttt90) cc_final: 0.8540 (ttt90) REVERT: C 411 MET cc_start: 0.8468 (mmt) cc_final: 0.7924 (mtm) REVERT: C 425 ARG cc_start: 0.6784 (mtm-85) cc_final: 0.6158 (mmp-170) REVERT: C 467 ARG cc_start: 0.7911 (ttt90) cc_final: 0.7631 (ttt-90) REVERT: C 470 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7127 (ttm170) REVERT: D 164 SER cc_start: 0.8568 (t) cc_final: 0.8268 (t) REVERT: D 192 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7926 (mt-10) REVERT: D 293 LYS cc_start: 0.7794 (mmtt) cc_final: 0.6864 (mppt) REVERT: D 447 ARG cc_start: 0.7462 (ttp-110) cc_final: 0.6677 (tpt170) REVERT: D 468 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7065 (tptt) REVERT: E 35 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7977 (p) REVERT: E 39 SER cc_start: 0.8743 (t) cc_final: 0.8436 (p) REVERT: G 39 SER cc_start: 0.8659 (t) cc_final: 0.8394 (p) REVERT: G 110 MET cc_start: 0.6943 (mmt) cc_final: 0.5707 (ppp) REVERT: H 14 LYS cc_start: 0.7758 (mttt) cc_final: 0.6846 (tptt) REVERT: H 73 MET cc_start: 0.8034 (mmp) cc_final: 0.7688 (mmp) outliers start: 23 outliers final: 16 residues processed: 268 average time/residue: 0.1447 time to fit residues: 56.5470 Evaluate side-chains 279 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS B 448 HIS C 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.165422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.122793 restraints weight = 16824.208| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.80 r_work: 0.3219 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16461 Z= 0.137 Angle : 0.454 12.523 22262 Z= 0.235 Chirality : 0.038 0.173 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.445 18.322 2225 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.35 % Allowed : 14.49 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.29 (0.19), residues: 2030 helix: 2.57 (0.13), residues: 1565 sheet: 0.32 (0.65), residues: 64 loop : 0.96 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 447 TYR 0.016 0.001 TYR B 245 PHE 0.011 0.001 PHE A 356 TRP 0.008 0.001 TRP D 350 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00319 (16457) covalent geometry : angle 0.45443 (22254) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.23912 ( 8) hydrogen bonds : bond 0.03679 ( 1195) hydrogen bonds : angle 3.05609 ( 3489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 269 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 377 LEU cc_start: 0.8382 (tp) cc_final: 0.8017 (mp) REVERT: A 404 LYS cc_start: 0.8557 (mttt) cc_final: 0.7769 (mmmt) REVERT: A 411 MET cc_start: 0.8679 (mmt) cc_final: 0.8002 (mtm) REVERT: A 447 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.7054 (tpt170) REVERT: B 165 LEU cc_start: 0.8177 (tp) cc_final: 0.7708 (tt) REVERT: B 461 GLN cc_start: 0.7940 (mm110) cc_final: 0.7609 (mt0) REVERT: B 467 ARG cc_start: 0.7562 (ttt90) cc_final: 0.7039 (ttp80) REVERT: B 468 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8071 (mttt) REVERT: B 470 ARG cc_start: 0.7587 (mmp80) cc_final: 0.7140 (mmp80) REVERT: C 411 MET cc_start: 0.8477 (mmt) cc_final: 0.7956 (mtm) REVERT: C 425 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6193 (mmp-170) REVERT: C 467 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7700 (ttt-90) REVERT: D 293 LYS cc_start: 0.7818 (mmtt) cc_final: 0.6940 (mppt) REVERT: D 447 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.6685 (tpt170) REVERT: D 468 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7070 (tptt) REVERT: E 35 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7992 (p) REVERT: E 39 SER cc_start: 0.8732 (t) cc_final: 0.8390 (p) REVERT: G 39 SER cc_start: 0.8699 (t) cc_final: 0.8461 (p) REVERT: G 65 ASP cc_start: 0.7973 (p0) cc_final: 0.7661 (p0) REVERT: G 110 MET cc_start: 0.6828 (mmt) cc_final: 0.5709 (ppp) REVERT: H 14 LYS cc_start: 0.7851 (mttt) cc_final: 0.6932 (tptt) REVERT: H 73 MET cc_start: 0.8092 (mmp) cc_final: 0.7719 (mmp) outliers start: 23 outliers final: 19 residues processed: 282 average time/residue: 0.1432 time to fit residues: 59.1746 Evaluate side-chains 278 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 52 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 188 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 448 HIS B 448 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.163568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120594 restraints weight = 16837.925| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.80 r_work: 0.3213 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16461 Z= 0.143 Angle : 0.471 12.252 22262 Z= 0.242 Chirality : 0.038 0.174 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.496 18.879 2225 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.35 % Allowed : 14.72 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.19), residues: 2030 helix: 2.56 (0.13), residues: 1565 sheet: 0.26 (0.64), residues: 64 loop : 0.92 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 447 TYR 0.018 0.001 TYR B 245 PHE 0.012 0.001 PHE A 356 TRP 0.009 0.001 TRP A 431 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00335 (16457) covalent geometry : angle 0.47115 (22254) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.24531 ( 8) hydrogen bonds : bond 0.03744 ( 1195) hydrogen bonds : angle 3.08068 ( 3489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8260 (tp) REVERT: A 377 LEU cc_start: 0.8390 (tp) cc_final: 0.8021 (mp) REVERT: A 404 LYS cc_start: 0.8556 (mttt) cc_final: 0.7764 (mmmt) REVERT: A 411 MET cc_start: 0.8693 (mmt) cc_final: 0.8004 (mtm) REVERT: A 447 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.7037 (tpt170) REVERT: B 165 LEU cc_start: 0.8186 (tp) cc_final: 0.7718 (tt) REVERT: B 447 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.6327 (ttm-80) REVERT: B 461 GLN cc_start: 0.7930 (mm110) cc_final: 0.7587 (mt0) REVERT: B 467 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7044 (ttp80) REVERT: B 468 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8053 (mttt) REVERT: B 470 ARG cc_start: 0.7578 (mmp80) cc_final: 0.7127 (mmp80) REVERT: C 330 ARG cc_start: 0.8869 (ttt90) cc_final: 0.8625 (ttt90) REVERT: C 411 MET cc_start: 0.8453 (mmt) cc_final: 0.7952 (mtm) REVERT: C 425 ARG cc_start: 0.6836 (mtm-85) cc_final: 0.6179 (mmp-170) REVERT: C 467 ARG cc_start: 0.7961 (ttt90) cc_final: 0.7704 (ttt-90) REVERT: D 293 LYS cc_start: 0.7769 (mmtt) cc_final: 0.6918 (mppt) REVERT: D 447 ARG cc_start: 0.7508 (ttp-110) cc_final: 0.6673 (tpt170) REVERT: D 468 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7054 (tptt) REVERT: E 35 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (p) REVERT: E 39 SER cc_start: 0.8729 (t) cc_final: 0.8356 (p) REVERT: F 29 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7081 (p) REVERT: G 39 SER cc_start: 0.8693 (t) cc_final: 0.8455 (p) REVERT: G 110 MET cc_start: 0.6804 (mmt) cc_final: 0.5706 (ppp) REVERT: H 14 LYS cc_start: 0.7853 (mttt) cc_final: 0.6937 (tptt) REVERT: H 73 MET cc_start: 0.8091 (mmp) cc_final: 0.7723 (mmp) outliers start: 23 outliers final: 17 residues processed: 273 average time/residue: 0.1461 time to fit residues: 58.2268 Evaluate side-chains 275 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS B 448 HIS C 232 ASN F 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.165958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123013 restraints weight = 16729.566| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.85 r_work: 0.3197 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16461 Z= 0.119 Angle : 0.470 12.202 22262 Z= 0.237 Chirality : 0.037 0.169 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.445 18.084 2225 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.52 % Allowed : 14.49 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.40 (0.19), residues: 2030 helix: 2.74 (0.13), residues: 1541 sheet: 0.28 (0.65), residues: 64 loop : 0.72 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.018 0.001 TYR B 245 PHE 0.010 0.001 PHE A 356 TRP 0.009 0.001 TRP B 327 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00270 (16457) covalent geometry : angle 0.47004 (22254) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.25694 ( 8) hydrogen bonds : bond 0.03523 ( 1195) hydrogen bonds : angle 3.02882 ( 3489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8798 (tmm) cc_final: 0.8418 (tmm) REVERT: A 222 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8214 (tp) REVERT: A 377 LEU cc_start: 0.8331 (tp) cc_final: 0.7951 (mp) REVERT: A 404 LYS cc_start: 0.8442 (mttt) cc_final: 0.7632 (mmmt) REVERT: A 411 MET cc_start: 0.8648 (mmt) cc_final: 0.7935 (mtm) REVERT: A 447 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.6991 (tpt170) REVERT: B 165 LEU cc_start: 0.8164 (tp) cc_final: 0.7682 (tt) REVERT: B 461 GLN cc_start: 0.7882 (mm110) cc_final: 0.7524 (mt0) REVERT: B 467 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7012 (ttp80) REVERT: B 468 LYS cc_start: 0.8351 (ttmm) cc_final: 0.7994 (mttt) REVERT: B 470 ARG cc_start: 0.7543 (mmp80) cc_final: 0.7086 (mmp80) REVERT: C 330 ARG cc_start: 0.8818 (ttt90) cc_final: 0.8584 (ttt90) REVERT: C 340 ASP cc_start: 0.7882 (t70) cc_final: 0.7560 (t0) REVERT: C 411 MET cc_start: 0.8429 (mmt) cc_final: 0.7868 (mtm) REVERT: C 425 ARG cc_start: 0.6775 (mtm-85) cc_final: 0.6094 (mmp-170) REVERT: C 467 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7640 (ttt-90) REVERT: D 293 LYS cc_start: 0.7716 (mmtt) cc_final: 0.6822 (mppt) REVERT: D 447 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.6593 (tpt170) REVERT: D 468 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7034 (tptt) REVERT: E 35 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7929 (p) REVERT: E 39 SER cc_start: 0.8699 (t) cc_final: 0.8365 (p) REVERT: F 29 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7010 (p) REVERT: G 39 SER cc_start: 0.8649 (t) cc_final: 0.8382 (p) REVERT: G 110 MET cc_start: 0.6700 (mmt) cc_final: 0.5608 (ppp) REVERT: H 14 LYS cc_start: 0.7790 (mttt) cc_final: 0.6855 (tptt) REVERT: H 73 MET cc_start: 0.8015 (mmp) cc_final: 0.7675 (mmp) outliers start: 26 outliers final: 21 residues processed: 274 average time/residue: 0.1426 time to fit residues: 57.1831 Evaluate side-chains 278 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 73 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 81 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS B 448 HIS C 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.166197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123242 restraints weight = 16675.599| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.85 r_work: 0.3195 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16461 Z= 0.115 Angle : 0.464 13.990 22262 Z= 0.234 Chirality : 0.037 0.168 2582 Planarity : 0.003 0.039 2803 Dihedral : 3.430 18.037 2225 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.47 % Allowed : 14.43 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.19), residues: 2030 helix: 2.79 (0.13), residues: 1541 sheet: 0.29 (0.66), residues: 64 loop : 0.75 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.018 0.001 TYR B 245 PHE 0.010 0.001 PHE A 356 TRP 0.009 0.001 TRP B 327 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00260 (16457) covalent geometry : angle 0.46386 (22254) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.24173 ( 8) hydrogen bonds : bond 0.03475 ( 1195) hydrogen bonds : angle 3.01119 ( 3489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.45 seconds wall clock time: 77 minutes 47.15 seconds (4667.15 seconds total)