Starting phenix.real_space_refine on Wed Mar 4 03:20:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kak_22773/03_2026/7kak_22773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kak_22773/03_2026/7kak_22773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kak_22773/03_2026/7kak_22773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kak_22773/03_2026/7kak_22773.map" model { file = "/net/cci-nas-00/data/ceres_data/7kak_22773/03_2026/7kak_22773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kak_22773/03_2026/7kak_22773.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.055 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 6796 2.51 5 N 1789 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10437 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3331 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'HIS:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3612 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 31, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1355 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.45, per 1000 atoms: 0.23 Number of scatterers: 10437 At special positions: 0 Unit cell: (107.16, 125.4, 136.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1803 8.00 N 1789 7.00 C 6796 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: 1.02 Conformation dependent library (CDL) restraints added in 541.4 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 67.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.506A pdb=" N ILE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 136 removed outlier: 3.985A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.142A pdb=" N GLY A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.101A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 4.271A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.570A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.511A pdb=" N GLN A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 4.271A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.942A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.890A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.979A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 463 removed outlier: 3.589A pdb=" N ILE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 68 removed outlier: 3.677A pdb=" N PHE C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Proline residue: C 61 - end of helix removed outlier: 3.611A pdb=" N ALA C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 removed outlier: 3.842A pdb=" N VAL B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 56 through 68 removed outlier: 4.151A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 97 removed outlier: 4.204A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.753A pdb=" N ILE D 196 " --> pdb=" O PRO D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 228 removed outlier: 4.578A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.700A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 4.032A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.881A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.675A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.826A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 332 through 357 removed outlier: 4.067A pdb=" N GLU D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 removed outlier: 3.664A pdb=" N GLN D 375 " --> pdb=" O GLN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.572A pdb=" N LEU D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 387' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.818A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 71 through 104 removed outlier: 4.315A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 138 removed outlier: 3.652A pdb=" N GLN E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 3.934A pdb=" N PHE E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'F' and resid 31 through 56 removed outlier: 4.108A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 87 removed outlier: 4.604A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 113 through 135 removed outlier: 4.108A pdb=" N ALA F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.618A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.768A pdb=" N GLU A 210 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 7 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.548A pdb=" N TYR A 281 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.613A pdb=" N VAL A 325 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 448 through 457 removed outlier: 5.975A pdb=" N ILE D 450 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG D 476 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 454 " --> pdb=" O VAL D 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 565 removed outlier: 5.942A pdb=" N LEU D 550 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 548 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 549 " --> pdb=" O HIS D 604 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 617 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 15 677 hydrogen bonds defined for protein. 2016 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: 1.57 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3307 1.34 - 1.46: 2203 1.46 - 1.58: 5075 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10670 Sorted by residual: bond pdb=" C PRO F 57 " pdb=" N PRO F 58 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.25e-02 6.40e+03 4.57e+00 bond pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 1.471 1.458 0.013 1.29e-02 6.01e+03 9.96e-01 bond pdb=" CB PRO D 536 " pdb=" CG PRO D 536 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.43e-01 bond pdb=" CA ILE D 361 " pdb=" CB ILE D 361 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.15e-01 bond pdb=" C LEU D 28 " pdb=" O LEU D 28 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.00e-02 1.00e+04 5.80e-01 ... (remaining 10665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 14307 1.79 - 3.58: 160 3.58 - 5.37: 29 5.37 - 7.16: 8 7.16 - 8.95: 2 Bond angle restraints: 14506 Sorted by residual: angle pdb=" N PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta sigma weight residual 103.44 110.15 -6.71 1.12e+00 7.97e-01 3.59e+01 angle pdb=" CA LEU D 28 " pdb=" C LEU D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 120.77 116.97 3.80 9.70e-01 1.06e+00 1.54e+01 angle pdb=" N SER A 289 " pdb=" CA SER A 289 " pdb=" C SER A 289 " ideal model delta sigma weight residual 111.02 114.52 -3.50 1.22e+00 6.72e-01 8.24e+00 angle pdb=" C ILE A 417 " pdb=" CA ILE A 417 " pdb=" CB ILE A 417 " ideal model delta sigma weight residual 114.00 110.53 3.47 1.31e+00 5.83e-01 7.01e+00 angle pdb=" CA LEU A 63 " pdb=" CB LEU A 63 " pdb=" CG LEU A 63 " ideal model delta sigma weight residual 116.30 125.25 -8.95 3.50e+00 8.16e-02 6.54e+00 ... (remaining 14501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5940 17.85 - 35.70: 382 35.70 - 53.56: 50 53.56 - 71.41: 5 71.41 - 89.26: 4 Dihedral angle restraints: 6381 sinusoidal: 2413 harmonic: 3968 Sorted by residual: dihedral pdb=" CB GLU A 169 " pdb=" CG GLU A 169 " pdb=" CD GLU A 169 " pdb=" OE1 GLU A 169 " ideal model delta sinusoidal sigma weight residual 0.00 89.26 -89.26 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta harmonic sigma weight residual 115.10 122.79 -7.69 0 2.50e+00 1.60e-01 9.47e+00 dihedral pdb=" CA ARG E 48 " pdb=" CB ARG E 48 " pdb=" CG ARG E 48 " pdb=" CD ARG E 48 " ideal model delta sinusoidal sigma weight residual -60.00 -110.93 50.93 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1379 0.046 - 0.092: 270 0.092 - 0.138: 40 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA THR A 83 " pdb=" N THR A 83 " pdb=" C THR A 83 " pdb=" CB THR A 83 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1688 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.020 2.00e-02 2.50e+03 1.30e-02 4.24e+00 pdb=" CG TRP E 141 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 426 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 427 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 56 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO F 57 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.025 5.00e-02 4.00e+02 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2176 2.78 - 3.31: 10222 3.31 - 3.84: 16711 3.84 - 4.37: 16831 4.37 - 4.90: 30500 Nonbonded interactions: 76440 Sorted by model distance: nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 53 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU A 79 " pdb=" OH TYR A 139 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 155 " pdb=" NH2 ARG E 159 " model vdw 2.291 3.120 nonbonded pdb=" NH1 ARG E 159 " pdb=" O ALA F 106 " model vdw 2.293 3.120 nonbonded pdb=" O SER D 228 " pdb=" OG SER D 228 " model vdw 2.296 3.040 ... (remaining 76435 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10670 Z= 0.121 Angle : 0.543 8.951 14506 Z= 0.291 Chirality : 0.037 0.230 1691 Planarity : 0.004 0.047 1816 Dihedral : 11.574 89.261 3819 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1341 helix: -0.01 (0.17), residues: 871 sheet: -2.04 (0.60), residues: 63 loop : -2.52 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 540 TYR 0.006 0.001 TYR E 51 PHE 0.011 0.001 PHE E 42 TRP 0.034 0.001 TRP E 141 HIS 0.004 0.001 HIS C 59 Details of bonding type rmsd covalent geometry : bond 0.00252 (10670) covalent geometry : angle 0.54291 (14506) hydrogen bonds : bond 0.11197 ( 677) hydrogen bonds : angle 4.62827 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8841 (tmm) cc_final: 0.7619 (mmp) REVERT: A 125 LEU cc_start: 0.9782 (tt) cc_final: 0.9554 (pp) REVERT: A 131 CYS cc_start: 0.9122 (m) cc_final: 0.8727 (m) REVERT: D 217 LEU cc_start: 0.9299 (tp) cc_final: 0.9096 (tt) REVERT: E 121 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9104 (pttt) REVERT: E 162 MET cc_start: 0.9115 (tpp) cc_final: 0.8902 (tpp) REVERT: F 177 ARG cc_start: 0.9150 (mtp-110) cc_final: 0.8686 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1275 time to fit residues: 25.6524 Evaluate side-chains 98 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 156 GLN A 261 GLN D 61 GLN D 444 GLN D 529 GLN D 604 HIS E 95 GLN F 30 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041122 restraints weight = 74504.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042149 restraints weight = 41222.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042837 restraints weight = 27927.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043226 restraints weight = 21528.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.043556 restraints weight = 18311.539| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10670 Z= 0.233 Angle : 0.661 10.435 14506 Z= 0.323 Chirality : 0.039 0.126 1691 Planarity : 0.005 0.054 1816 Dihedral : 3.445 14.683 1474 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.42 % Allowed : 12.48 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.23), residues: 1341 helix: 1.09 (0.18), residues: 885 sheet: -1.90 (0.62), residues: 73 loop : -1.99 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 80 TYR 0.016 0.001 TYR F 100 PHE 0.022 0.002 PHE E 42 TRP 0.022 0.001 TRP E 141 HIS 0.005 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00514 (10670) covalent geometry : angle 0.66055 (14506) hydrogen bonds : bond 0.03961 ( 677) hydrogen bonds : angle 4.00164 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8942 (tmm) cc_final: 0.7506 (mmp) REVERT: A 69 MET cc_start: 0.9410 (tpp) cc_final: 0.9187 (tpp) REVERT: A 78 MET cc_start: 0.8703 (mmm) cc_final: 0.8351 (mmm) REVERT: A 131 CYS cc_start: 0.9364 (m) cc_final: 0.8850 (m) REVERT: E 162 MET cc_start: 0.9346 (tpp) cc_final: 0.9143 (tpp) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.1054 time to fit residues: 16.6269 Evaluate side-chains 99 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 HIS ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 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 = 0.3179 r_free = 0.3179 target = 0.050639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039947 restraints weight = 75715.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.040933 restraints weight = 41399.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.041604 restraints weight = 28109.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042032 restraints weight = 21680.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042294 restraints weight = 18301.831| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10670 Z= 0.260 Angle : 0.681 10.450 14506 Z= 0.336 Chirality : 0.039 0.178 1691 Planarity : 0.005 0.070 1816 Dihedral : 3.759 17.693 1474 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.46 % Allowed : 17.01 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1341 helix: 1.46 (0.18), residues: 888 sheet: -1.65 (0.64), residues: 73 loop : -1.77 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 50 TYR 0.009 0.001 TYR E 51 PHE 0.021 0.002 PHE E 42 TRP 0.017 0.002 TRP E 141 HIS 0.007 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00571 (10670) covalent geometry : angle 0.68097 (14506) hydrogen bonds : bond 0.04254 ( 677) hydrogen bonds : angle 4.11782 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8952 (tmm) cc_final: 0.7478 (mmp) REVERT: A 131 CYS cc_start: 0.9360 (m) cc_final: 0.8868 (m) REVERT: A 368 MET cc_start: 0.8994 (tpt) cc_final: 0.8627 (tpt) REVERT: D 252 MET cc_start: 0.9099 (ppp) cc_final: 0.8855 (ppp) REVERT: D 369 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9247 (tp) REVERT: E 162 MET cc_start: 0.9310 (tpp) cc_final: 0.9068 (tpp) REVERT: F 137 MET cc_start: 0.8086 (mpp) cc_final: 0.7796 (pmm) outliers start: 26 outliers final: 14 residues processed: 110 average time/residue: 0.0893 time to fit residues: 14.8073 Evaluate side-chains 99 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 43 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 = 0.3174 r_free = 0.3174 target = 0.050318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.039825 restraints weight = 75110.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.040825 restraints weight = 40808.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041473 restraints weight = 27549.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.041857 restraints weight = 21348.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042179 restraints weight = 18168.741| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10670 Z= 0.242 Angle : 0.668 10.987 14506 Z= 0.326 Chirality : 0.039 0.167 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.775 17.019 1474 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 19.47 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.23), residues: 1341 helix: 1.65 (0.18), residues: 879 sheet: -1.50 (0.65), residues: 73 loop : -1.61 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.020 0.001 TYR F 100 PHE 0.019 0.002 PHE E 42 TRP 0.013 0.001 TRP E 141 HIS 0.006 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00534 (10670) covalent geometry : angle 0.66821 (14506) hydrogen bonds : bond 0.04136 ( 677) hydrogen bonds : angle 4.04925 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8999 (tmm) cc_final: 0.7526 (mmp) REVERT: A 131 CYS cc_start: 0.9368 (m) cc_final: 0.8889 (m) REVERT: A 166 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9339 (tt) REVERT: A 368 MET cc_start: 0.9031 (tpt) cc_final: 0.8744 (tpt) REVERT: D 252 MET cc_start: 0.9095 (ppp) cc_final: 0.7917 (ppp) REVERT: D 369 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9228 (tp) REVERT: E 162 MET cc_start: 0.9294 (tpp) cc_final: 0.8983 (tpp) outliers start: 29 outliers final: 20 residues processed: 112 average time/residue: 0.0844 time to fit residues: 14.3553 Evaluate side-chains 103 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 116 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.040204 restraints weight = 74867.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.041230 restraints weight = 40393.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.041869 restraints weight = 27178.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.042296 restraints weight = 21064.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042551 restraints weight = 17770.110| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10670 Z= 0.175 Angle : 0.617 11.023 14506 Z= 0.297 Chirality : 0.038 0.168 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.651 18.252 1474 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.02 % Allowed : 19.94 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1341 helix: 1.88 (0.18), residues: 874 sheet: -1.26 (0.66), residues: 73 loop : -1.46 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.016 0.001 TYR E 12 PHE 0.015 0.001 PHE E 42 TRP 0.010 0.001 TRP E 141 HIS 0.005 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00390 (10670) covalent geometry : angle 0.61727 (14506) hydrogen bonds : bond 0.03941 ( 677) hydrogen bonds : angle 3.84138 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9001 (tmm) cc_final: 0.7451 (mmp) REVERT: A 69 MET cc_start: 0.9475 (tpp) cc_final: 0.9158 (tpp) REVERT: A 131 CYS cc_start: 0.9376 (m) cc_final: 0.8900 (m) REVERT: A 166 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9329 (tt) REVERT: D 252 MET cc_start: 0.9098 (ppp) cc_final: 0.7992 (ppp) REVERT: E 121 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8923 (pttp) REVERT: E 162 MET cc_start: 0.9265 (tpp) cc_final: 0.8913 (tpp) outliers start: 32 outliers final: 18 residues processed: 115 average time/residue: 0.0841 time to fit residues: 14.7809 Evaluate side-chains 101 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 116 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.050898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040470 restraints weight = 75388.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.041505 restraints weight = 40323.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042179 restraints weight = 27045.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042569 restraints weight = 20740.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.042899 restraints weight = 17608.462| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10670 Z= 0.134 Angle : 0.624 13.718 14506 Z= 0.293 Chirality : 0.038 0.175 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.526 16.945 1474 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.46 % Allowed : 22.40 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.24), residues: 1341 helix: 1.97 (0.18), residues: 874 sheet: -1.02 (0.66), residues: 75 loop : -1.34 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.017 0.001 TYR C 53 PHE 0.013 0.001 PHE E 42 TRP 0.009 0.001 TRP E 176 HIS 0.004 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00302 (10670) covalent geometry : angle 0.62365 (14506) hydrogen bonds : bond 0.03753 ( 677) hydrogen bonds : angle 3.72962 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8984 (tmm) cc_final: 0.7395 (mmp) REVERT: A 69 MET cc_start: 0.9471 (tpp) cc_final: 0.9193 (tpp) REVERT: A 78 MET cc_start: 0.8696 (mmm) cc_final: 0.8144 (tpp) REVERT: A 131 CYS cc_start: 0.9381 (m) cc_final: 0.8903 (m) REVERT: A 166 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9334 (tt) REVERT: D 252 MET cc_start: 0.9075 (ppp) cc_final: 0.7920 (ppp) REVERT: E 121 LYS cc_start: 0.9287 (mtmm) cc_final: 0.8965 (pttp) REVERT: E 162 MET cc_start: 0.9256 (tpp) cc_final: 0.8882 (tpp) outliers start: 26 outliers final: 18 residues processed: 108 average time/residue: 0.0895 time to fit residues: 14.7073 Evaluate side-chains 102 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 43 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 = 0.3176 r_free = 0.3176 target = 0.050286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.039873 restraints weight = 74159.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.040877 restraints weight = 40213.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041534 restraints weight = 27123.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.041931 restraints weight = 20939.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.042244 restraints weight = 17784.635| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10670 Z= 0.187 Angle : 0.642 12.095 14506 Z= 0.308 Chirality : 0.038 0.175 1691 Planarity : 0.004 0.048 1816 Dihedral : 3.599 17.600 1474 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.12 % Allowed : 22.31 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1341 helix: 1.96 (0.18), residues: 876 sheet: -0.91 (0.66), residues: 75 loop : -1.30 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 128 TYR 0.011 0.001 TYR E 12 PHE 0.017 0.001 PHE E 42 TRP 0.012 0.001 TRP E 141 HIS 0.005 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00416 (10670) covalent geometry : angle 0.64221 (14506) hydrogen bonds : bond 0.03879 ( 677) hydrogen bonds : angle 3.81059 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9001 (tmm) cc_final: 0.7450 (mmp) REVERT: A 69 MET cc_start: 0.9474 (tpp) cc_final: 0.9200 (tpp) REVERT: A 78 MET cc_start: 0.8849 (mmm) cc_final: 0.8285 (tpp) REVERT: A 131 CYS cc_start: 0.9411 (m) cc_final: 0.8952 (m) REVERT: A 166 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9337 (tt) REVERT: D 252 MET cc_start: 0.9113 (ppp) cc_final: 0.7686 (ppp) REVERT: E 121 LYS cc_start: 0.9372 (mtmm) cc_final: 0.9019 (pttp) REVERT: E 162 MET cc_start: 0.9291 (tpp) cc_final: 0.8974 (tpp) outliers start: 33 outliers final: 24 residues processed: 109 average time/residue: 0.0908 time to fit residues: 14.9248 Evaluate side-chains 108 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 101 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.040280 restraints weight = 74705.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.041303 restraints weight = 40410.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041983 restraints weight = 27240.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042415 restraints weight = 20895.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042663 restraints weight = 17634.572| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10670 Z= 0.150 Angle : 0.633 12.027 14506 Z= 0.299 Chirality : 0.038 0.182 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.571 18.936 1474 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.02 % Allowed : 22.21 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1341 helix: 2.06 (0.18), residues: 875 sheet: -0.74 (0.67), residues: 75 loop : -1.23 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 128 TYR 0.011 0.001 TYR E 12 PHE 0.013 0.001 PHE E 42 TRP 0.012 0.001 TRP E 141 HIS 0.004 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00336 (10670) covalent geometry : angle 0.63311 (14506) hydrogen bonds : bond 0.03738 ( 677) hydrogen bonds : angle 3.70839 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9025 (tmm) cc_final: 0.7462 (mmp) REVERT: A 69 MET cc_start: 0.9477 (tpp) cc_final: 0.9228 (tpp) REVERT: A 78 MET cc_start: 0.8700 (mmm) cc_final: 0.8207 (tpp) REVERT: A 131 CYS cc_start: 0.9401 (m) cc_final: 0.8934 (m) REVERT: A 166 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9342 (tt) REVERT: D 252 MET cc_start: 0.9085 (ppp) cc_final: 0.8695 (ppp) REVERT: E 23 PHE cc_start: 0.9263 (t80) cc_final: 0.9007 (t80) REVERT: E 162 MET cc_start: 0.9271 (tpp) cc_final: 0.8920 (tpp) outliers start: 32 outliers final: 24 residues processed: 115 average time/residue: 0.0881 time to fit residues: 15.6491 Evaluate side-chains 108 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.049887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.039418 restraints weight = 75443.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.040413 restraints weight = 41625.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.041055 restraints weight = 28149.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041452 restraints weight = 21841.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.041743 restraints weight = 18553.152| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10670 Z= 0.215 Angle : 0.681 11.627 14506 Z= 0.326 Chirality : 0.039 0.168 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.714 19.771 1474 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.74 % Allowed : 22.97 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1341 helix: 2.06 (0.18), residues: 878 sheet: -1.14 (0.61), residues: 85 loop : -1.19 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 128 TYR 0.019 0.001 TYR C 53 PHE 0.017 0.002 PHE E 42 TRP 0.012 0.001 TRP E 141 HIS 0.005 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00477 (10670) covalent geometry : angle 0.68099 (14506) hydrogen bonds : bond 0.03992 ( 677) hydrogen bonds : angle 3.88309 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9003 (tmm) cc_final: 0.7483 (mmp) REVERT: A 69 MET cc_start: 0.9493 (tpp) cc_final: 0.9234 (tpp) REVERT: A 78 MET cc_start: 0.8869 (mmm) cc_final: 0.8308 (tpp) REVERT: A 166 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9342 (tt) REVERT: A 401 MET cc_start: 0.7714 (pmm) cc_final: 0.6969 (ptp) REVERT: D 252 MET cc_start: 0.9076 (ppp) cc_final: 0.8602 (ppp) REVERT: D 588 MET cc_start: 0.8215 (tpt) cc_final: 0.7967 (tpt) REVERT: E 23 PHE cc_start: 0.9319 (t80) cc_final: 0.9067 (t80) REVERT: E 121 LYS cc_start: 0.9267 (pttp) cc_final: 0.9049 (mtmm) REVERT: E 162 MET cc_start: 0.9290 (tpp) cc_final: 0.8989 (tpp) outliers start: 29 outliers final: 25 residues processed: 107 average time/residue: 0.0829 time to fit residues: 13.6217 Evaluate side-chains 107 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.040511 restraints weight = 74200.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041528 restraints weight = 40217.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042216 restraints weight = 27114.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042618 restraints weight = 20731.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.042961 restraints weight = 17531.544| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10670 Z= 0.134 Angle : 0.645 11.911 14506 Z= 0.303 Chirality : 0.038 0.173 1691 Planarity : 0.004 0.050 1816 Dihedral : 3.603 20.401 1474 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 23.72 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1341 helix: 2.14 (0.18), residues: 875 sheet: -0.71 (0.66), residues: 75 loop : -1.13 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 128 TYR 0.017 0.001 TYR C 53 PHE 0.013 0.001 PHE D 15 TRP 0.013 0.001 TRP E 141 HIS 0.004 0.001 HIS D 534 Details of bonding type rmsd covalent geometry : bond 0.00303 (10670) covalent geometry : angle 0.64493 (14506) hydrogen bonds : bond 0.03719 ( 677) hydrogen bonds : angle 3.67488 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8998 (tmm) cc_final: 0.7404 (mmp) REVERT: A 69 MET cc_start: 0.9489 (tpp) cc_final: 0.9239 (tpp) REVERT: A 78 MET cc_start: 0.8770 (mmm) cc_final: 0.8320 (tpp) REVERT: A 166 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9336 (tt) REVERT: A 401 MET cc_start: 0.7735 (pmm) cc_final: 0.7026 (ptp) REVERT: D 252 MET cc_start: 0.9113 (ppp) cc_final: 0.8233 (ppp) REVERT: E 23 PHE cc_start: 0.9229 (t80) cc_final: 0.8957 (t80) REVERT: E 162 MET cc_start: 0.9225 (tpp) cc_final: 0.8813 (tpp) outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.0898 time to fit residues: 13.8346 Evaluate side-chains 102 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 0.0370 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.041906 restraints weight = 74463.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042948 restraints weight = 40549.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.043667 restraints weight = 26949.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044143 restraints weight = 20499.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044410 restraints weight = 17071.840| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10670 Z= 0.113 Angle : 0.654 11.918 14506 Z= 0.305 Chirality : 0.038 0.194 1691 Planarity : 0.004 0.051 1816 Dihedral : 3.464 20.933 1474 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.42 % Allowed : 24.48 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1341 helix: 2.13 (0.18), residues: 876 sheet: -0.62 (0.65), residues: 75 loop : -1.07 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.017 0.001 TYR C 53 PHE 0.026 0.001 PHE B 106 TRP 0.012 0.001 TRP E 141 HIS 0.006 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00250 (10670) covalent geometry : angle 0.65449 (14506) hydrogen bonds : bond 0.03395 ( 677) hydrogen bonds : angle 3.55150 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.84 seconds wall clock time: 29 minutes 17.05 seconds (1757.05 seconds total)