Starting phenix.real_space_refine on Fri Mar 15 04:22:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahd_11783/03_2024/7ahd_11783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahd_11783/03_2024/7ahd_11783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahd_11783/03_2024/7ahd_11783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahd_11783/03_2024/7ahd_11783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahd_11783/03_2024/7ahd_11783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahd_11783/03_2024/7ahd_11783_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 50 5.16 5 C 6805 2.51 5 N 1762 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 33": "OE1" <-> "OE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10562 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4170 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 525} Chain breaks: 2 Chain: "D" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "B" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2184 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'BET': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.00, per 1000 atoms: 0.57 Number of scatterers: 10562 At special positions: 0 Unit cell: (92.092, 83.996, 136.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 6 15.00 O 1939 8.00 N 1762 7.00 C 6805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 8 sheets defined 61.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 123 through 126 No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 129 through 132 No H-bonds generated for 'chain 'C' and resid 129 through 132' Processing helix chain 'C' and resid 138 through 152 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'A' and resid 11 through 25 Processing helix chain 'A' and resid 28 through 50 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 91 through 121 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.033A pdb=" N LYS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 143 through 152 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 205 through 226 removed outlier: 5.215A pdb=" N GLY A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.835A pdb=" N ILE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 252 through 276 removed outlier: 4.560A pdb=" N LEU A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 331 through 347 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 489 through 492 No H-bonds generated for 'chain 'A' and resid 489 through 492' Processing helix chain 'A' and resid 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.246A pdb=" N VAL A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 549 Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'D' and resid 18 through 27 Processing helix chain 'D' and resid 31 through 38 Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 129 through 132 No H-bonds generated for 'chain 'D' and resid 129 through 132' Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 197 through 213 Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 27 through 50 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 91 through 120 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.711A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 141 through 151 removed outlier: 3.889A pdb=" N ILE B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Proline residue: B 147 - end of helix Processing helix chain 'B' and resid 157 through 179 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 205 through 234 removed outlier: 5.701A pdb=" N GLY B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 252 through 277 removed outlier: 3.716A pdb=" N LEU B 276 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 309 Processing sheet with id= A, first strand: chain 'C' and resid 49 through 51 Processing sheet with id= B, first strand: chain 'C' and resid 242 through 245 removed outlier: 6.780A pdb=" N ILE C 237 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 234 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 218 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 59 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE C 220 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLY C 61 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 322 through 328 removed outlier: 6.509A pdb=" N ASP A 350 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LEU A 325 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS A 352 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TYR A 327 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR A 354 " --> pdb=" O TYR A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 376 through 378 removed outlier: 4.061A pdb=" N GLY A 397 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 515 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU A 395 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 480 through 485 Processing sheet with id= F, first strand: chain 'A' and resid 428 through 430 removed outlier: 6.258A pdb=" N LYS A 456 " --> pdb=" O ILE A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= H, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.779A pdb=" N ILE D 237 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 234 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 218 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 59 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE D 220 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N GLY D 61 " --> pdb=" O PHE D 220 " (cutoff:3.500A) 581 hydrogen bonds defined for protein. 1707 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: 2.97 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1864 1.32 - 1.45: 2492 1.45 - 1.57: 6279 1.57 - 1.70: 1 1.70 - 1.82: 106 Bond restraints: 10742 Sorted by residual: bond pdb=" O5' ATP C 501 " pdb=" PA ATP C 501 " ideal model delta sigma weight residual 1.579 1.820 -0.241 1.10e-02 8.26e+03 4.80e+02 bond pdb=" O5' ATP D 501 " pdb=" PA ATP D 501 " ideal model delta sigma weight residual 1.579 1.819 -0.240 1.10e-02 8.26e+03 4.78e+02 bond pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 1.592 1.784 -0.192 1.10e-02 8.26e+03 3.04e+02 bond pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 1.592 1.783 -0.191 1.10e-02 8.26e+03 3.03e+02 bond pdb=" C5' ATP D 501 " pdb=" O5' ATP D 501 " ideal model delta sigma weight residual 1.443 1.344 0.099 1.00e-02 1.00e+04 9.71e+01 ... (remaining 10737 not shown) Histogram of bond angle deviations from ideal: 91.13 - 99.71: 23 99.71 - 108.29: 462 108.29 - 116.87: 7285 116.87 - 125.45: 6612 125.45 - 134.03: 162 Bond angle restraints: 14544 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 105.64 34.23 1.00e+00 1.00e+00 1.17e+03 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 105.68 34.19 1.00e+00 1.00e+00 1.17e+03 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 105.44 31.39 1.00e+00 1.00e+00 9.85e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 105.47 31.36 1.00e+00 1.00e+00 9.83e+02 angle pdb=" C5' ATP D 501 " pdb=" O5' ATP D 501 " pdb=" PA ATP D 501 " ideal model delta sigma weight residual 121.27 104.61 16.66 1.00e+00 1.00e+00 2.78e+02 ... (remaining 14539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 5897 16.69 - 33.38: 477 33.38 - 50.06: 96 50.06 - 66.75: 39 66.75 - 83.44: 6 Dihedral angle restraints: 6515 sinusoidal: 2636 harmonic: 3879 Sorted by residual: dihedral pdb=" CA TRP A 535 " pdb=" C TRP A 535 " pdb=" N THR A 536 " pdb=" CA THR A 536 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN C 215 " pdb=" C GLN C 215 " pdb=" N LYS C 216 " pdb=" CA LYS C 216 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLN D 215 " pdb=" C GLN D 215 " pdb=" N LYS D 216 " pdb=" CA LYS D 216 " ideal model delta harmonic sigma weight residual 180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1686 0.106 - 0.212: 41 0.212 - 0.317: 0 0.317 - 0.423: 0 0.423 - 0.529: 2 Chirality restraints: 1729 Sorted by residual: chirality pdb=" CB THR D 122 " pdb=" CA THR D 122 " pdb=" OG1 THR D 122 " pdb=" CG2 THR D 122 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB THR C 122 " pdb=" CA THR C 122 " pdb=" OG1 THR C 122 " pdb=" CG2 THR C 122 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA LEU D 225 " pdb=" N LEU D 225 " pdb=" C LEU D 225 " pdb=" CB LEU D 225 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1726 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 142 " 0.109 9.50e-02 1.11e+02 5.50e-02 9.22e+00 pdb=" NE ARG C 142 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 142 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG C 142 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 142 " 0.108 9.50e-02 1.11e+02 5.44e-02 9.15e+00 pdb=" NE ARG D 142 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 142 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG D 142 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 260 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C TYR C 260 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR C 260 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 261 " -0.014 2.00e-02 2.50e+03 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1581 2.75 - 3.29: 11325 3.29 - 3.83: 17329 3.83 - 4.36: 21578 4.36 - 4.90: 37206 Nonbonded interactions: 89019 Sorted by model distance: nonbonded pdb=" OD1 ASP A 134 " pdb=" NH2 ARG A 173 " model vdw 2.215 2.520 nonbonded pdb=" NZ LYS A 321 " pdb=" O GLY A 348 " model vdw 2.216 2.520 nonbonded pdb=" NE2 GLN A 385 " pdb=" O GLN B 248 " model vdw 2.228 2.520 nonbonded pdb=" OG1 THR B 171 " pdb=" OG1 THR B 220 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR A 381 " pdb=" OE2 GLU A 509 " model vdw 2.264 2.440 ... (remaining 89014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.260 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 10742 Z= 0.589 Angle : 1.096 34.229 14544 Z= 0.771 Chirality : 0.049 0.529 1729 Planarity : 0.004 0.055 1805 Dihedral : 13.541 83.441 4007 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.79 % Allowed : 1.22 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1347 helix: 0.81 (0.18), residues: 858 sheet: -1.97 (0.44), residues: 117 loop : -1.51 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 535 HIS 0.004 0.001 HIS A 382 PHE 0.024 0.001 PHE B 161 TYR 0.012 0.002 TYR A 493 ARG 0.048 0.002 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.7337 (mmm) cc_final: 0.7101 (mmt) REVERT: A 290 LYS cc_start: 0.4636 (pttm) cc_final: 0.4367 (pttm) REVERT: D 62 LEU cc_start: 0.8074 (mp) cc_final: 0.7595 (mp) REVERT: D 101 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7667 (mt) outliers start: 9 outliers final: 1 residues processed: 178 average time/residue: 0.3219 time to fit residues: 75.8435 Evaluate side-chains 94 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 ASN C 151 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10742 Z= 0.242 Angle : 0.569 7.174 14544 Z= 0.291 Chirality : 0.042 0.153 1729 Planarity : 0.004 0.050 1805 Dihedral : 6.843 82.679 1488 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.87 % Allowed : 6.64 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1347 helix: 1.39 (0.18), residues: 857 sheet: -1.38 (0.46), residues: 119 loop : -1.18 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 535 HIS 0.003 0.001 HIS C 9 PHE 0.021 0.001 PHE B 161 TYR 0.009 0.001 TYR A 144 ARG 0.003 0.001 ARG C 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: C 201 ARG cc_start: 0.6777 (ttp-110) cc_final: 0.6544 (mtm-85) REVERT: A 290 LYS cc_start: 0.4579 (pttm) cc_final: 0.4228 (pttm) REVERT: A 413 MET cc_start: 0.6817 (mtp) cc_final: 0.6337 (mtt) REVERT: A 471 GLU cc_start: 0.7407 (mp0) cc_final: 0.7052 (mp0) REVERT: D 101 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7762 (mp) REVERT: D 201 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7180 (mtm180) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.2393 time to fit residues: 41.9870 Evaluate side-chains 110 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN C 134 GLN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10742 Z= 0.206 Angle : 0.518 8.628 14544 Z= 0.264 Chirality : 0.041 0.201 1729 Planarity : 0.004 0.049 1805 Dihedral : 6.841 88.480 1488 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.83 % Allowed : 7.69 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1347 helix: 1.58 (0.18), residues: 858 sheet: -1.22 (0.47), residues: 119 loop : -1.18 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.002 0.001 HIS A 476 PHE 0.021 0.001 PHE A 151 TYR 0.011 0.001 TYR D 260 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: C 201 ARG cc_start: 0.6949 (ttp-110) cc_final: 0.6691 (mtm-85) REVERT: C 239 LYS cc_start: 0.6222 (mttt) cc_final: 0.5425 (ttmm) REVERT: A 290 LYS cc_start: 0.4466 (pttm) cc_final: 0.4092 (pttm) REVERT: A 471 GLU cc_start: 0.7702 (mp0) cc_final: 0.7267 (mp0) REVERT: D 101 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7926 (mp) REVERT: D 201 ARG cc_start: 0.7386 (ttm110) cc_final: 0.7120 (mtm180) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.2195 time to fit residues: 39.8061 Evaluate side-chains 110 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10742 Z= 0.364 Angle : 0.604 8.162 14544 Z= 0.307 Chirality : 0.044 0.186 1729 Planarity : 0.004 0.054 1805 Dihedral : 6.924 84.260 1488 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 9.17 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1347 helix: 1.37 (0.18), residues: 853 sheet: -1.28 (0.47), residues: 119 loop : -1.20 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.004 0.001 HIS A 347 PHE 0.018 0.002 PHE C 49 TYR 0.010 0.002 TYR D 260 ARG 0.003 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7691 (tp30) cc_final: 0.7408 (tp30) REVERT: A 290 LYS cc_start: 0.4488 (pttm) cc_final: 0.4134 (pttm) REVERT: A 471 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7521 (mp0) outliers start: 31 outliers final: 19 residues processed: 132 average time/residue: 0.2365 time to fit residues: 43.7848 Evaluate side-chains 124 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 260 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN C 134 GLN C 181 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10742 Z= 0.346 Angle : 0.580 8.461 14544 Z= 0.295 Chirality : 0.043 0.160 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.728 85.313 1486 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 10.66 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1347 helix: 1.30 (0.18), residues: 856 sheet: -1.27 (0.47), residues: 117 loop : -1.28 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.002 PHE C 49 TYR 0.014 0.002 TYR D 260 ARG 0.003 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: C 96 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7914 (p0) REVERT: C 239 LYS cc_start: 0.6367 (mttt) cc_final: 0.5588 (ttmm) REVERT: A 185 GLU cc_start: 0.7735 (tp30) cc_final: 0.7463 (tp30) REVERT: A 290 LYS cc_start: 0.4602 (pttm) cc_final: 0.4260 (pttm) REVERT: A 471 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: B 106 LEU cc_start: 0.8803 (tp) cc_final: 0.8190 (mt) outliers start: 27 outliers final: 21 residues processed: 128 average time/residue: 0.2322 time to fit residues: 41.8773 Evaluate side-chains 130 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 181 ASN A 87 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10742 Z= 0.213 Angle : 0.524 8.420 14544 Z= 0.266 Chirality : 0.041 0.150 1729 Planarity : 0.004 0.050 1805 Dihedral : 6.681 87.670 1486 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.27 % Allowed : 11.35 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1347 helix: 1.51 (0.18), residues: 855 sheet: -1.17 (0.48), residues: 117 loop : -1.19 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.001 0.000 HIS A 564 PHE 0.014 0.001 PHE C 49 TYR 0.015 0.001 TYR D 260 ARG 0.001 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: C 96 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7987 (p0) REVERT: C 239 LYS cc_start: 0.6292 (mttt) cc_final: 0.5496 (ttmm) REVERT: A 185 GLU cc_start: 0.7742 (tp30) cc_final: 0.7461 (tp30) REVERT: A 471 GLU cc_start: 0.8190 (mp0) cc_final: 0.7954 (mm-30) REVERT: B 56 MET cc_start: 0.7933 (tpp) cc_final: 0.7587 (tpp) REVERT: B 106 LEU cc_start: 0.8794 (tp) cc_final: 0.8174 (mt) outliers start: 26 outliers final: 18 residues processed: 134 average time/residue: 0.2307 time to fit residues: 44.4117 Evaluate side-chains 127 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10742 Z= 0.211 Angle : 0.539 11.843 14544 Z= 0.271 Chirality : 0.041 0.155 1729 Planarity : 0.004 0.049 1805 Dihedral : 6.604 87.589 1486 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.45 % Allowed : 11.88 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1347 helix: 1.58 (0.18), residues: 856 sheet: -1.23 (0.47), residues: 121 loop : -1.12 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.001 0.000 HIS A 564 PHE 0.013 0.001 PHE C 49 TYR 0.014 0.002 TYR D 45 ARG 0.001 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.152 Fit side-chains REVERT: C 96 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.8023 (p0) REVERT: C 239 LYS cc_start: 0.6288 (mttt) cc_final: 0.5479 (ttmm) REVERT: A 185 GLU cc_start: 0.7707 (tp30) cc_final: 0.7468 (tp30) REVERT: A 471 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: B 106 LEU cc_start: 0.8827 (tp) cc_final: 0.8205 (mt) outliers start: 28 outliers final: 22 residues processed: 128 average time/residue: 0.2221 time to fit residues: 41.3981 Evaluate side-chains 127 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10742 Z= 0.221 Angle : 0.528 8.521 14544 Z= 0.268 Chirality : 0.041 0.170 1729 Planarity : 0.004 0.049 1805 Dihedral : 6.580 87.516 1486 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.36 % Allowed : 12.31 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1347 helix: 1.55 (0.18), residues: 869 sheet: -1.24 (0.47), residues: 121 loop : -1.09 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.001 0.000 HIS A 347 PHE 0.013 0.001 PHE A 572 TYR 0.013 0.001 TYR D 260 ARG 0.003 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: C 96 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8049 (p0) REVERT: C 239 LYS cc_start: 0.6279 (mttt) cc_final: 0.5485 (ttmm) REVERT: A 185 GLU cc_start: 0.7733 (tp30) cc_final: 0.7492 (tp30) REVERT: A 449 TYR cc_start: 0.8571 (m-80) cc_final: 0.8292 (m-80) REVERT: A 471 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: B 56 MET cc_start: 0.7971 (tpp) cc_final: 0.7628 (tpp) REVERT: B 106 LEU cc_start: 0.8837 (tp) cc_final: 0.8209 (mt) outliers start: 27 outliers final: 24 residues processed: 124 average time/residue: 0.2065 time to fit residues: 37.4975 Evaluate side-chains 131 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 102 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10742 Z= 0.235 Angle : 0.532 8.883 14544 Z= 0.269 Chirality : 0.041 0.154 1729 Planarity : 0.004 0.048 1805 Dihedral : 6.566 87.158 1486 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.53 % Allowed : 12.31 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1347 helix: 1.58 (0.18), residues: 869 sheet: -1.22 (0.48), residues: 117 loop : -1.05 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.002 0.001 HIS A 564 PHE 0.013 0.001 PHE C 49 TYR 0.014 0.002 TYR D 260 ARG 0.001 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.284 Fit side-chains REVERT: C 239 LYS cc_start: 0.6322 (mttt) cc_final: 0.5498 (ttmm) REVERT: A 185 GLU cc_start: 0.7756 (tp30) cc_final: 0.7519 (tp30) REVERT: A 449 TYR cc_start: 0.8546 (m-80) cc_final: 0.8222 (m-80) REVERT: B 56 MET cc_start: 0.7925 (tpp) cc_final: 0.7570 (tpp) REVERT: B 106 LEU cc_start: 0.8851 (tp) cc_final: 0.8214 (mt) outliers start: 29 outliers final: 21 residues processed: 134 average time/residue: 0.2150 time to fit residues: 41.7405 Evaluate side-chains 125 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10742 Z= 0.304 Angle : 0.570 9.393 14544 Z= 0.288 Chirality : 0.043 0.184 1729 Planarity : 0.004 0.049 1805 Dihedral : 6.629 86.014 1486 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.01 % Allowed : 12.75 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1347 helix: 1.51 (0.18), residues: 868 sheet: -1.49 (0.46), residues: 121 loop : -1.07 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.002 0.001 HIS C 223 PHE 0.015 0.001 PHE C 49 TYR 0.015 0.002 TYR D 260 ARG 0.003 0.000 ARG C 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: C 239 LYS cc_start: 0.6338 (mttt) cc_final: 0.5528 (ttmm) REVERT: A 185 GLU cc_start: 0.7792 (tp30) cc_final: 0.7556 (tp30) REVERT: A 449 TYR cc_start: 0.8586 (m-80) cc_final: 0.8234 (m-80) REVERT: A 505 MET cc_start: 0.7541 (mmm) cc_final: 0.7139 (mmm) REVERT: B 106 LEU cc_start: 0.8877 (tp) cc_final: 0.8223 (mt) outliers start: 23 outliers final: 23 residues processed: 122 average time/residue: 0.2165 time to fit residues: 38.0635 Evaluate side-chains 124 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.092805 restraints weight = 15962.789| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.44 r_work: 0.2911 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10742 Z= 0.297 Angle : 0.573 9.324 14544 Z= 0.290 Chirality : 0.043 0.221 1729 Planarity : 0.004 0.049 1805 Dihedral : 6.674 86.553 1486 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.27 % Allowed : 12.58 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1347 helix: 1.50 (0.18), residues: 868 sheet: -1.67 (0.49), residues: 108 loop : -1.07 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.002 0.001 HIS C 223 PHE 0.015 0.001 PHE C 49 TYR 0.015 0.002 TYR D 260 ARG 0.006 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.12 seconds wall clock time: 38 minutes 19.25 seconds (2299.25 seconds total)