Starting phenix.real_space_refine on Wed Jul 30 09:53:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahh_11786/07_2025/7ahh_11786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahh_11786/07_2025/7ahh_11786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ahh_11786/07_2025/7ahh_11786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahh_11786/07_2025/7ahh_11786.map" model { file = "/net/cci-nas-00/data/ceres_data/7ahh_11786/07_2025/7ahh_11786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahh_11786/07_2025/7ahh_11786.cif" } resolution = 3.5 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= 0.006 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 8 5.49 5 S 60 5.16 5 C 7763 2.51 5 N 2024 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12125 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4011 Classifications: {'peptide': 526} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain: "C" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "D" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2992 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'BET': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'2BA': 1, 'ANP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 7.33, per 1000 atoms: 0.60 Number of scatterers: 12125 At special positions: 0 Unit cell: (93.104, 100.188, 150.788, 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 60 16.00 P 8 15.00 O 2270 8.00 N 2024 7.00 C 7763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2894 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 63.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 91 through 121 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.929A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix removed outlier: 3.662A pdb=" N THR A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.155A pdb=" N TYR A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) 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 183 through 193 removed outlier: 3.565A pdb=" N VAL A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.543A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 3.860A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 275 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.582A pdb=" N ALA A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.687A pdb=" N GLY A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 423 through 426 removed outlier: 4.097A pdb=" N ASN A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.191A pdb=" N ASP A 454 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 476 removed outlier: 3.580A pdb=" N VAL A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 518 through 522 Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 539 through 549 removed outlier: 4.265A pdb=" N VAL A 543 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.576A pdb=" N ILE A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.680A pdb=" N TRP A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 26 Processing helix chain 'B' and resid 26 through 51 removed outlier: 3.629A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 91 through 122 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.577A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.206A pdb=" N TYR B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.191A 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 156 through 181 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 204 through 232 removed outlier: 3.698A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLY B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.006A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 275 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 122 through 133 removed outlier: 4.679A pdb=" N GLY C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 152 through 153 No H-bonds generated for 'chain 'C' and resid 152 through 153' Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.316A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.950A pdb=" N ALA C 194 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 292 through 304 Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.921A pdb=" N TYR C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.884A pdb=" N GLU C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 122 through 133 removed outlier: 4.680A pdb=" N GLY D 130 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'D' and resid 152 through 153 No H-bonds generated for 'chain 'D' and resid 152 through 153' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.316A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 3.950A pdb=" N ALA D 194 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 292 through 304 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 356 through 363 removed outlier: 3.921A pdb=" N TYR D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.885A pdb=" N GLU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 322 through 327 Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 378 removed outlier: 5.607A pdb=" N VAL A 374 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 514 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 376 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 400 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 481 through 484 removed outlier: 3.612A pdb=" N GLY A 406 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 430 removed outlier: 6.104A pdb=" N ILE A 429 " --> pdb=" O VAL A 458 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR C 45 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS C 12 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR C 45 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS C 12 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 10 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 82 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.581A pdb=" N MET C 60 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET C 244 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'C' and resid 285 through 287 Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 370 removed outlier: 4.143A pdb=" N GLY C 378 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR D 45 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS D 12 " --> pdb=" O TYR D 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 47 removed outlier: 5.618A pdb=" N TYR D 45 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS D 12 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU D 10 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER D 82 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 60 through 61 removed outlier: 6.581A pdb=" N MET D 60 " --> pdb=" O MET D 238 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET D 244 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 370 removed outlier: 4.143A pdb=" N GLY D 378 " --> pdb=" O VAL D 369 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3432 1.33 - 1.45: 1700 1.45 - 1.57: 7057 1.57 - 1.69: 16 1.69 - 1.81: 120 Bond restraints: 12325 Sorted by residual: bond pdb=" N3B ANP C 501 " pdb=" PG ANP C 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" N3B ANP D 501 " pdb=" PG ANP D 501 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" O3A ANP D 501 " pdb=" PB ANP D 501 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ANP C 501 " pdb=" PB ANP C 501 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C5' 2BA D 502 " pdb=" O5' 2BA D 502 " ideal model delta sigma weight residual 1.433 1.359 0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 12320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 16026 2.05 - 4.10: 526 4.10 - 6.15: 110 6.15 - 8.20: 27 8.20 - 10.25: 18 Bond angle restraints: 16707 Sorted by residual: angle pdb=" N ILE C 252 " pdb=" CA ILE C 252 " pdb=" C ILE C 252 " ideal model delta sigma weight residual 111.00 103.52 7.48 1.09e+00 8.42e-01 4.71e+01 angle pdb=" N LEU C 253 " pdb=" CA LEU C 253 " pdb=" C LEU C 253 " ideal model delta sigma weight residual 112.23 120.87 -8.64 1.26e+00 6.30e-01 4.70e+01 angle pdb=" N ILE D 252 " pdb=" CA ILE D 252 " pdb=" C ILE D 252 " ideal model delta sigma weight residual 111.00 103.64 7.36 1.09e+00 8.42e-01 4.56e+01 angle pdb=" N LEU D 253 " pdb=" CA LEU D 253 " pdb=" C LEU D 253 " ideal model delta sigma weight residual 112.23 120.06 -7.83 1.26e+00 6.30e-01 3.86e+01 angle pdb=" CA THR A 537 " pdb=" CB THR A 537 " pdb=" CG2 THR A 537 " ideal model delta sigma weight residual 110.50 119.06 -8.56 1.70e+00 3.46e-01 2.54e+01 ... (remaining 16702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 6981 19.56 - 39.12: 442 39.12 - 58.68: 97 58.68 - 78.24: 20 78.24 - 97.80: 14 Dihedral angle restraints: 7554 sinusoidal: 3086 harmonic: 4468 Sorted by residual: dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N LYS A 538 " pdb=" CA LYS A 538 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA SER C 109 " pdb=" C SER C 109 " pdb=" N MET C 110 " pdb=" CA MET C 110 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER D 109 " pdb=" C SER D 109 " pdb=" N MET D 110 " pdb=" CA MET D 110 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1984 0.230 - 0.460: 7 0.460 - 0.691: 8 0.691 - 0.921: 0 0.921 - 1.151: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CB THR A 537 " pdb=" CA THR A 537 " pdb=" OG1 THR A 537 " pdb=" CG2 THR A 537 " both_signs ideal model delta sigma weight residual False 2.55 1.40 1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CG LEU C 101 " pdb=" CB LEU C 101 " pdb=" CD1 LEU C 101 " pdb=" CD2 LEU C 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" CG LEU D 101 " pdb=" CB LEU D 101 " pdb=" CD1 LEU D 101 " pdb=" CD2 LEU D 101 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.57e+00 ... (remaining 1997 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " 0.029 2.00e-02 2.50e+03 3.42e-02 2.04e+01 pdb=" CG PHE C 214 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 214 " 0.028 2.00e-02 2.50e+03 3.38e-02 2.00e+01 pdb=" CG PHE D 214 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE D 214 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE D 214 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 214 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 214 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 214 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 169 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO A 170 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.043 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1846 2.75 - 3.29: 13180 3.29 - 3.83: 19435 3.83 - 4.36: 23880 4.36 - 4.90: 40952 Nonbonded interactions: 99293 Sorted by model distance: nonbonded pdb=" O GLU C 250 " pdb=" N LEU C 253 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP D 91 " pdb=" N VAL D 92 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP C 91 " pdb=" N VAL C 92 " model vdw 2.227 3.120 nonbonded pdb=" N HIS C 9 " pdb=" OD1 ASN C 48 " model vdw 2.228 3.120 nonbonded pdb=" N HIS D 9 " pdb=" OD1 ASN D 48 " model vdw 2.228 3.120 ... (remaining 99288 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 'C' selection = (chain 'D' and (resid 3 through 391 or resid 501)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 0.164 12325 Z= 0.356 Angle : 0.967 10.253 16707 Z= 0.534 Chirality : 0.067 1.151 2000 Planarity : 0.005 0.076 2084 Dihedral : 14.623 97.804 4660 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.23 % Allowed : 2.27 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1548 helix: 0.24 (0.18), residues: 870 sheet: -4.26 (0.33), residues: 124 loop : -2.24 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 535 HIS 0.004 0.001 HIS D 9 PHE 0.077 0.003 PHE C 214 TYR 0.013 0.002 TYR A 327 ARG 0.017 0.001 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.17609 ( 671) hydrogen bonds : angle 6.84547 ( 1941) covalent geometry : bond 0.00800 (12325) covalent geometry : angle 0.96673 (16707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 1.326 Fit side-chains REVERT: A 119 MET cc_start: 0.8231 (ttm) cc_final: 0.7932 (mtp) REVERT: A 198 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7554 (ttp-110) REVERT: D 45 TYR cc_start: 0.7776 (t80) cc_final: 0.7342 (t80) REVERT: D 109 SER cc_start: 0.8889 (t) cc_final: 0.8683 (t) REVERT: D 189 ASP cc_start: 0.7543 (t0) cc_final: 0.7277 (t0) outliers start: 3 outliers final: 0 residues processed: 239 average time/residue: 0.2683 time to fit residues: 89.6062 Evaluate side-chains 153 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 387 GLN A 451 ASN B 8 GLN C 126 ASN C 151 ASN D 126 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117170 restraints weight = 18703.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119769 restraints weight = 10826.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121547 restraints weight = 7411.019| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12325 Z= 0.162 Angle : 0.670 10.848 16707 Z= 0.348 Chirality : 0.045 0.176 2000 Planarity : 0.005 0.052 2084 Dihedral : 7.848 60.884 1753 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.06 % Allowed : 7.87 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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 (0.22), residues: 1548 helix: 0.87 (0.18), residues: 883 sheet: -3.70 (0.35), residues: 130 loop : -1.69 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 535 HIS 0.003 0.001 HIS A 476 PHE 0.015 0.001 PHE C 214 TYR 0.016 0.001 TYR A 412 ARG 0.007 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 671) hydrogen bonds : angle 4.89684 ( 1941) covalent geometry : bond 0.00346 (12325) covalent geometry : angle 0.66997 (16707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 1.352 Fit side-chains REVERT: D 45 TYR cc_start: 0.7697 (t80) cc_final: 0.7246 (t80) REVERT: D 101 LEU cc_start: 0.8260 (tp) cc_final: 0.8055 (tp) REVERT: D 189 ASP cc_start: 0.7456 (t0) cc_final: 0.7245 (t0) outliers start: 14 outliers final: 5 residues processed: 192 average time/residue: 0.2044 time to fit residues: 60.2081 Evaluate side-chains 151 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 88 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN C 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114571 restraints weight = 18956.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117111 restraints weight = 11102.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118836 restraints weight = 7695.633| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12325 Z= 0.136 Angle : 0.595 7.233 16707 Z= 0.304 Chirality : 0.044 0.161 2000 Planarity : 0.004 0.052 2084 Dihedral : 7.125 59.793 1753 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.06 % Allowed : 10.21 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.33 (0.22), residues: 1548 helix: 0.99 (0.18), residues: 899 sheet: -3.23 (0.36), residues: 130 loop : -1.46 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.002 0.000 HIS A 476 PHE 0.014 0.001 PHE A 349 TYR 0.011 0.001 TYR A 412 ARG 0.004 0.000 ARG C 121 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 671) hydrogen bonds : angle 4.54722 ( 1941) covalent geometry : bond 0.00318 (12325) covalent geometry : angle 0.59474 (16707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.390 Fit side-chains REVERT: A 119 MET cc_start: 0.8289 (ttm) cc_final: 0.7849 (mtp) REVERT: A 328 MET cc_start: 0.8151 (mpp) cc_final: 0.7810 (mtt) REVERT: A 356 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7441 (pp) REVERT: C 60 MET cc_start: 0.7984 (mtp) cc_final: 0.7699 (mtp) REVERT: D 45 TYR cc_start: 0.7749 (t80) cc_final: 0.7215 (t80) outliers start: 14 outliers final: 9 residues processed: 163 average time/residue: 0.2078 time to fit residues: 51.9350 Evaluate side-chains 151 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 11 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN C 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113731 restraints weight = 18821.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116241 restraints weight = 11154.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117953 restraints weight = 7779.930| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12325 Z= 0.124 Angle : 0.565 9.246 16707 Z= 0.287 Chirality : 0.043 0.156 2000 Planarity : 0.004 0.048 2084 Dihedral : 6.805 59.922 1753 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.74 % Allowed : 10.89 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.02 (0.22), residues: 1548 helix: 1.21 (0.18), residues: 898 sheet: -2.84 (0.37), residues: 134 loop : -1.34 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.001 0.000 HIS A 476 PHE 0.016 0.001 PHE A 349 TYR 0.011 0.001 TYR A 412 ARG 0.002 0.000 ARG D 234 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 671) hydrogen bonds : angle 4.35033 ( 1941) covalent geometry : bond 0.00287 (12325) covalent geometry : angle 0.56518 (16707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 2.268 Fit side-chains REVERT: A 119 MET cc_start: 0.8307 (ttm) cc_final: 0.7873 (mtp) REVERT: A 328 MET cc_start: 0.8192 (mpp) cc_final: 0.7895 (mtt) REVERT: B 185 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: D 45 TYR cc_start: 0.7759 (t80) cc_final: 0.7151 (t80) REVERT: D 60 MET cc_start: 0.8443 (mtp) cc_final: 0.7741 (mtm) outliers start: 23 outliers final: 12 residues processed: 172 average time/residue: 0.2108 time to fit residues: 56.2553 Evaluate side-chains 158 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS C 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100489 restraints weight = 19713.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103185 restraints weight = 11107.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104982 restraints weight = 7576.067| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12325 Z= 0.184 Angle : 0.610 8.645 16707 Z= 0.310 Chirality : 0.045 0.146 2000 Planarity : 0.004 0.046 2084 Dihedral : 6.611 69.286 1753 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.50 % Allowed : 12.93 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.09 (0.22), residues: 1548 helix: 1.12 (0.18), residues: 896 sheet: -2.61 (0.40), residues: 134 loop : -1.37 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 535 HIS 0.002 0.001 HIS C 223 PHE 0.015 0.001 PHE D 49 TYR 0.015 0.001 TYR A 327 ARG 0.004 0.000 ARG C 230 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 671) hydrogen bonds : angle 4.38976 ( 1941) covalent geometry : bond 0.00449 (12325) covalent geometry : angle 0.61025 (16707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.850 Fit side-chains REVERT: A 119 MET cc_start: 0.8566 (ttm) cc_final: 0.8214 (mtp) REVERT: A 416 ASN cc_start: 0.8243 (t0) cc_final: 0.7715 (m-40) REVERT: B 185 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: C 60 MET cc_start: 0.7865 (mtp) cc_final: 0.7406 (mtp) REVERT: D 11 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8704 (m) REVERT: D 45 TYR cc_start: 0.7986 (t80) cc_final: 0.7149 (t80) outliers start: 33 outliers final: 19 residues processed: 177 average time/residue: 0.2454 time to fit residues: 65.5561 Evaluate side-chains 167 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 347 HIS C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106845 restraints weight = 19618.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109442 restraints weight = 11386.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111231 restraints weight = 7869.312| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12325 Z= 0.140 Angle : 0.576 8.699 16707 Z= 0.292 Chirality : 0.043 0.145 2000 Planarity : 0.004 0.045 2084 Dihedral : 6.454 69.530 1753 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 14.60 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.12 (0.22), residues: 1548 helix: 1.27 (0.18), residues: 895 sheet: -2.46 (0.41), residues: 132 loop : -1.27 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.001 0.000 HIS A 487 PHE 0.011 0.001 PHE C 49 TYR 0.020 0.001 TYR A 527 ARG 0.007 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 671) hydrogen bonds : angle 4.28674 ( 1941) covalent geometry : bond 0.00339 (12325) covalent geometry : angle 0.57586 (16707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 2.497 Fit side-chains REVERT: A 119 MET cc_start: 0.8486 (ttm) cc_final: 0.8115 (mtp) REVERT: A 416 ASN cc_start: 0.8229 (t0) cc_final: 0.7764 (m-40) REVERT: A 545 LEU cc_start: 0.8116 (pp) cc_final: 0.7855 (mm) REVERT: B 185 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: C 60 MET cc_start: 0.7928 (mtp) cc_final: 0.7401 (mtp) REVERT: D 11 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8718 (m) REVERT: D 45 TYR cc_start: 0.7936 (t80) cc_final: 0.7183 (t80) outliers start: 25 outliers final: 14 residues processed: 173 average time/residue: 0.2692 time to fit residues: 71.2478 Evaluate side-chains 162 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 105 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 62 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 52 ASN C 135 ASN C 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107598 restraints weight = 19428.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.110011 restraints weight = 11772.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111558 restraints weight = 8357.213| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12325 Z= 0.128 Angle : 0.574 8.621 16707 Z= 0.290 Chirality : 0.043 0.143 2000 Planarity : 0.004 0.045 2084 Dihedral : 6.368 70.232 1753 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.04 % Allowed : 16.19 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.29 (0.22), residues: 1548 helix: 1.41 (0.18), residues: 895 sheet: -2.39 (0.42), residues: 132 loop : -1.20 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 PHE 0.010 0.001 PHE C 49 TYR 0.015 0.001 TYR A 527 ARG 0.005 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 671) hydrogen bonds : angle 4.24480 ( 1941) covalent geometry : bond 0.00303 (12325) covalent geometry : angle 0.57428 (16707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 2.807 Fit side-chains REVERT: A 119 MET cc_start: 0.8453 (ttm) cc_final: 0.8079 (mtp) REVERT: A 416 ASN cc_start: 0.8241 (t0) cc_final: 0.7776 (m-40) REVERT: B 185 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: C 60 MET cc_start: 0.7893 (mtp) cc_final: 0.7371 (mtp) REVERT: D 11 THR cc_start: 0.9080 (t) cc_final: 0.8698 (m) REVERT: D 45 TYR cc_start: 0.7898 (t80) cc_final: 0.7262 (t80) outliers start: 27 outliers final: 13 residues processed: 173 average time/residue: 0.3394 time to fit residues: 90.7433 Evaluate side-chains 164 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN D 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108185 restraints weight = 19700.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110803 restraints weight = 11528.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112591 restraints weight = 8005.441| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12325 Z= 0.119 Angle : 0.570 8.578 16707 Z= 0.286 Chirality : 0.042 0.142 2000 Planarity : 0.004 0.044 2084 Dihedral : 6.269 70.043 1753 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.74 % Allowed : 16.79 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.42 (0.22), residues: 1548 helix: 1.51 (0.18), residues: 893 sheet: -2.25 (0.44), residues: 132 loop : -1.15 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 PHE 0.010 0.001 PHE C 49 TYR 0.013 0.001 TYR A 527 ARG 0.004 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 671) hydrogen bonds : angle 4.18020 ( 1941) covalent geometry : bond 0.00280 (12325) covalent geometry : angle 0.57041 (16707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.391 Fit side-chains REVERT: A 119 MET cc_start: 0.8446 (ttm) cc_final: 0.8066 (mtp) REVERT: A 416 ASN cc_start: 0.8290 (t0) cc_final: 0.7779 (m-40) REVERT: A 545 LEU cc_start: 0.8082 (pp) cc_final: 0.7865 (mm) REVERT: B 185 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: C 60 MET cc_start: 0.7919 (mtp) cc_final: 0.7339 (mtp) REVERT: D 11 THR cc_start: 0.9078 (t) cc_final: 0.8693 (m) REVERT: D 45 TYR cc_start: 0.7951 (t80) cc_final: 0.7373 (t80) outliers start: 23 outliers final: 17 residues processed: 168 average time/residue: 0.2301 time to fit residues: 60.0059 Evaluate side-chains 170 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107962 restraints weight = 19690.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110582 restraints weight = 11571.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112215 restraints weight = 8036.134| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12325 Z= 0.124 Angle : 0.570 8.552 16707 Z= 0.286 Chirality : 0.042 0.142 2000 Planarity : 0.004 0.044 2084 Dihedral : 6.227 71.124 1753 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.04 % Allowed : 16.49 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.50 (0.22), residues: 1548 helix: 1.58 (0.18), residues: 892 sheet: -2.18 (0.44), residues: 132 loop : -1.14 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 PHE 0.009 0.001 PHE D 49 TYR 0.009 0.001 TYR A 412 ARG 0.004 0.000 ARG C 230 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 671) hydrogen bonds : angle 4.15756 ( 1941) covalent geometry : bond 0.00296 (12325) covalent geometry : angle 0.57019 (16707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.747 Fit side-chains REVERT: A 119 MET cc_start: 0.8445 (ttm) cc_final: 0.8086 (mtp) REVERT: A 545 LEU cc_start: 0.8129 (pp) cc_final: 0.7429 (mt) REVERT: B 42 ASN cc_start: 0.8337 (m110) cc_final: 0.7949 (m110) REVERT: B 185 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: B 254 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8369 (mtpp) REVERT: C 60 MET cc_start: 0.7925 (mtp) cc_final: 0.7348 (mtp) REVERT: D 11 THR cc_start: 0.9071 (t) cc_final: 0.8690 (m) REVERT: D 45 TYR cc_start: 0.7971 (t80) cc_final: 0.7409 (t80) REVERT: D 300 MET cc_start: 0.8999 (mtt) cc_final: 0.8605 (mtt) outliers start: 27 outliers final: 23 residues processed: 172 average time/residue: 0.2769 time to fit residues: 75.0363 Evaluate side-chains 181 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 119 optimal weight: 0.0970 chunk 150 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108802 restraints weight = 19580.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111378 restraints weight = 11593.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113142 restraints weight = 8110.737| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12325 Z= 0.115 Angle : 0.579 9.685 16707 Z= 0.285 Chirality : 0.042 0.165 2000 Planarity : 0.004 0.043 2084 Dihedral : 6.188 70.637 1753 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.74 % Allowed : 17.40 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 0.59 (0.22), residues: 1548 helix: 1.63 (0.18), residues: 892 sheet: -1.97 (0.44), residues: 142 loop : -1.07 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 PHE 0.014 0.001 PHE D 86 TYR 0.009 0.001 TYR A 389 ARG 0.004 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 671) hydrogen bonds : angle 4.11021 ( 1941) covalent geometry : bond 0.00270 (12325) covalent geometry : angle 0.57864 (16707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 2.715 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8411 (ttm) cc_final: 0.8028 (mtp) REVERT: A 274 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: A 545 LEU cc_start: 0.8119 (pp) cc_final: 0.7475 (mt) REVERT: B 42 ASN cc_start: 0.8245 (m110) cc_final: 0.7882 (m110) REVERT: B 185 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: B 254 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8372 (mtpp) REVERT: C 60 MET cc_start: 0.7908 (mtp) cc_final: 0.7446 (mtp) REVERT: D 11 THR cc_start: 0.9057 (t) cc_final: 0.8698 (m) REVERT: D 45 TYR cc_start: 0.7976 (t80) cc_final: 0.7418 (t80) REVERT: D 300 MET cc_start: 0.8998 (mtt) cc_final: 0.8614 (mtt) outliers start: 23 outliers final: 19 residues processed: 173 average time/residue: 0.2576 time to fit residues: 69.6689 Evaluate side-chains 181 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 0.1980 chunk 113 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 151 optimal weight: 0.0050 chunk 33 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN C 135 ASN ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109030 restraints weight = 19638.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111714 restraints weight = 11393.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113526 restraints weight = 7834.282| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12325 Z= 0.114 Angle : 0.575 9.236 16707 Z= 0.283 Chirality : 0.042 0.140 2000 Planarity : 0.004 0.042 2084 Dihedral : 6.156 70.391 1753 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.89 % Allowed : 17.47 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1548 helix: 1.64 (0.18), residues: 894 sheet: -1.96 (0.44), residues: 142 loop : -1.05 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 PHE 0.011 0.001 PHE A 349 TYR 0.009 0.001 TYR A 389 ARG 0.004 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 671) hydrogen bonds : angle 4.08897 ( 1941) covalent geometry : bond 0.00268 (12325) covalent geometry : angle 0.57461 (16707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.65 seconds wall clock time: 76 minutes 33.81 seconds (4593.81 seconds total)