Starting phenix.real_space_refine on Fri Mar 14 03:37:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0f_36763/03_2025/8k0f_36763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0f_36763/03_2025/8k0f_36763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0f_36763/03_2025/8k0f_36763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0f_36763/03_2025/8k0f_36763.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0f_36763/03_2025/8k0f_36763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0f_36763/03_2025/8k0f_36763.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 50 5.16 5 C 6112 2.51 5 N 1632 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9595 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5137 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 33, 'TRANS': 605} Chain breaks: 2 Chain: "B" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2994 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "C" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1407 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' FE': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.50, per 1000 atoms: 0.57 Number of scatterers: 9595 At special positions: 0 Unit cell: (100.1, 127.6, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 50 16.00 O 1800 8.00 N 1632 7.00 C 6112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 600 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 540 " " NAG A 802 " - " ASN A 316 " " NAG B 501 " - " ASN B 87 " " NAG B 502 " - " ASN B 363 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 57.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.679A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 82 removed outlier: 3.603A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 125 removed outlier: 3.693A pdb=" N PHE A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.634A pdb=" N ASN A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.639A pdb=" N GLN A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.657A pdb=" N PHE A 197 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.626A pdb=" N GLN A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.667A pdb=" N ALA A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.646A pdb=" N LEU A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.737A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.771A pdb=" N ALA A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 359 through 384 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.530A pdb=" N VAL A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 428 removed outlier: 3.523A pdb=" N GLU A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.617A pdb=" N ALA A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.658A pdb=" N TYR A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.620A pdb=" N GLU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 41' Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 60 through 87 removed outlier: 4.031A pdb=" N ASN B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.983A pdb=" N SER B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 126 removed outlier: 3.678A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 126 " --> pdb=" O CYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 130 Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.338A pdb=" N PHE B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.827A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.534A pdb=" N LEU B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.505A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 258 through 264 Processing helix chain 'B' and resid 265 through 276 removed outlier: 4.247A pdb=" N GLN B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.518A pdb=" N LEU B 281 " --> pdb=" O CYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 310 through 325 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.667A pdb=" N HIS B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 352 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN B 353 " --> pdb=" O GLU B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 348 through 353' Processing helix chain 'B' and resid 355 through 379 removed outlier: 3.780A pdb=" N GLN B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.629A pdb=" N LEU C 130 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 131 " --> pdb=" O ALA C 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 131' Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.607A pdb=" N SER C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461 removed outlier: 5.734A pdb=" N LEU A 459 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP A 475 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A 647 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY A 667 " --> pdb=" O THR A 570 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR A 570 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG A 669 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS A 568 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA A 671 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 566 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA A 673 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A 564 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP A 675 " --> pdb=" O SER A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 458 through 461 removed outlier: 5.734A pdb=" N LEU A 459 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP A 475 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A 647 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP A 623 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 637 through 641 removed outlier: 3.537A pdb=" N ALA A 639 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 627 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.534A pdb=" N TYR B 288 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AA6, first strand: chain 'C' and resid 135 through 136 removed outlier: 4.422A pdb=" N VAL C 135 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 121 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN C 119 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 59 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL C 165 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP C 17 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS C 170 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 15 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 12 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 14 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 18 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY C 26 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE C 20 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASP C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 29 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 135 through 136 removed outlier: 4.422A pdb=" N VAL C 135 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 121 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN C 119 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 59 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL C 165 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP C 17 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS C 170 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 15 " --> pdb=" O CYS C 170 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3148 1.34 - 1.46: 2323 1.46 - 1.58: 4282 1.58 - 1.71: 2 1.71 - 1.83: 75 Bond restraints: 9830 Sorted by residual: bond pdb=" CG PRO A 605 " pdb=" CD PRO A 605 " ideal model delta sigma weight residual 1.503 1.270 0.233 3.40e-02 8.65e+02 4.71e+01 bond pdb=" CB PRO A 221 " pdb=" CG PRO A 221 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.04e+01 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" CG PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 1.503 1.403 0.100 3.40e-02 8.65e+02 8.63e+00 bond pdb=" N PRO A 605 " pdb=" CD PRO A 605 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 6.87e+00 ... (remaining 9825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 13169 2.61 - 5.21: 98 5.21 - 7.82: 18 7.82 - 10.43: 5 10.43 - 13.03: 2 Bond angle restraints: 13292 Sorted by residual: angle pdb=" N PRO A 605 " pdb=" CD PRO A 605 " pdb=" CG PRO A 605 " ideal model delta sigma weight residual 103.20 90.29 12.91 1.50e+00 4.44e-01 7.41e+01 angle pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" CD PRO A 221 " ideal model delta sigma weight residual 112.00 103.01 8.99 1.40e+00 5.10e-01 4.13e+01 angle pdb=" N PRO A 221 " pdb=" CD PRO A 221 " pdb=" CG PRO A 221 " ideal model delta sigma weight residual 103.20 94.41 8.79 1.50e+00 4.44e-01 3.44e+01 angle pdb=" N ASP C 67 " pdb=" CA ASP C 67 " pdb=" CB ASP C 67 " ideal model delta sigma weight residual 114.17 107.82 6.35 1.14e+00 7.69e-01 3.10e+01 angle pdb=" CA PRO A 605 " pdb=" N PRO A 605 " pdb=" CD PRO A 605 " ideal model delta sigma weight residual 112.00 104.49 7.51 1.40e+00 5.10e-01 2.88e+01 ... (remaining 13287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 5326 22.94 - 45.89: 524 45.89 - 68.83: 71 68.83 - 91.77: 15 91.77 - 114.72: 17 Dihedral angle restraints: 5953 sinusoidal: 2486 harmonic: 3467 Sorted by residual: dihedral pdb=" CA CYS A 79 " pdb=" C CYS A 79 " pdb=" N ALA A 80 " pdb=" CA ALA A 80 " ideal model delta harmonic sigma weight residual 180.00 148.92 31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 119 " pdb=" CB CYS A 119 " ideal model delta sinusoidal sigma weight residual -86.00 -123.60 37.60 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CA CYS A 123 " pdb=" C CYS A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual -180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1302 0.076 - 0.151: 98 0.151 - 0.227: 2 0.227 - 0.302: 0 0.302 - 0.378: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA CYS A 79 " pdb=" N CYS A 79 " pdb=" C CYS A 79 " pdb=" CB CYS A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA GLU A 234 " pdb=" N GLU A 234 " pdb=" C GLU A 234 " pdb=" CB GLU A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1400 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 220 " 0.053 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 221 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 604 " -0.046 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO A 605 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 67 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ASP C 67 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP C 67 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE C 68 " 0.012 2.00e-02 2.50e+03 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 94 2.67 - 3.23: 8599 3.23 - 3.79: 13975 3.79 - 4.34: 18385 4.34 - 4.90: 31702 Nonbonded interactions: 72755 Sorted by model distance: nonbonded pdb=" O MET B 180 " pdb=" ND2 ASN B 184 " model vdw 2.114 3.120 nonbonded pdb=" OG SER A 463 " pdb=" O GLY A 468 " model vdw 2.162 3.040 nonbonded pdb=" NE2 HIS A 659 " pdb="FE FE A 803 " model vdw 2.238 2.340 nonbonded pdb=" OD1 ASP A 589 " pdb="FE FE A 803 " model vdw 2.293 2.260 nonbonded pdb=" OG1 THR A 34 " pdb=" OD1 ASP A 36 " model vdw 2.311 3.040 ... (remaining 72750 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.004 0.233 9830 Z= 0.295 Angle : 0.620 13.032 13292 Z= 0.334 Chirality : 0.041 0.378 1403 Planarity : 0.005 0.076 1741 Dihedral : 18.659 114.716 3720 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1172 helix: 1.55 (0.21), residues: 625 sheet: -0.95 (0.54), residues: 88 loop : -1.53 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 345 HIS 0.004 0.000 HIS B 266 PHE 0.017 0.001 PHE C 121 TYR 0.031 0.001 TYR B 338 ARG 0.006 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.062 Fit side-chains REVERT: A 259 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7039 (mt-10) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2549 time to fit residues: 35.3590 Evaluate side-chains 93 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.0000 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 487 GLN B 184 ASN B 218 ASN C 95 ASN C 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.186811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153641 restraints weight = 10148.358| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.88 r_work: 0.3302 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9830 Z= 0.147 Angle : 0.540 11.182 13292 Z= 0.269 Chirality : 0.040 0.282 1403 Planarity : 0.004 0.045 1741 Dihedral : 7.565 84.031 1399 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.18 % Allowed : 14.75 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1172 helix: 2.06 (0.21), residues: 629 sheet: -0.42 (0.55), residues: 87 loop : -1.26 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.003 0.000 HIS C 62 PHE 0.015 0.001 PHE C 121 TYR 0.020 0.001 TYR B 338 ARG 0.003 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.969 Fit side-chains REVERT: A 677 THR cc_start: 0.9111 (p) cc_final: 0.7968 (m) REVERT: B 350 GLU cc_start: 0.6360 (mp0) cc_final: 0.5992 (tm-30) REVERT: C 67 ASP cc_start: 0.5894 (t0) cc_final: 0.5677 (t0) outliers start: 22 outliers final: 10 residues processed: 120 average time/residue: 0.2290 time to fit residues: 38.2905 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 487 GLN B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.217439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.187024 restraints weight = 10846.296| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.82 r_work: 0.3541 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9830 Z= 0.280 Angle : 0.560 9.733 13292 Z= 0.289 Chirality : 0.042 0.201 1403 Planarity : 0.004 0.050 1741 Dihedral : 6.221 65.046 1399 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 2.38 % Allowed : 15.74 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1172 helix: 2.09 (0.21), residues: 629 sheet: -0.51 (0.53), residues: 90 loop : -1.32 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.008 0.001 HIS B 266 PHE 0.021 0.002 PHE C 121 TYR 0.022 0.002 TYR B 338 ARG 0.003 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7190 (mp0) cc_final: 0.6593 (mp0) REVERT: A 234 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: B 184 ASN cc_start: 0.6651 (m110) cc_final: 0.6323 (m110) REVERT: B 334 ASN cc_start: 0.7432 (m-40) cc_final: 0.7078 (m-40) REVERT: B 350 GLU cc_start: 0.6355 (mp0) cc_final: 0.6148 (tm-30) REVERT: C 27 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7856 (mtp180) REVERT: C 67 ASP cc_start: 0.6114 (t0) cc_final: 0.5749 (t0) outliers start: 24 outliers final: 17 residues processed: 121 average time/residue: 0.2954 time to fit residues: 50.6800 Evaluate side-chains 111 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 88 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.214030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.189856 restraints weight = 10522.890| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.45 r_work: 0.3628 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9830 Z= 0.159 Angle : 0.501 9.156 13292 Z= 0.255 Chirality : 0.039 0.153 1403 Planarity : 0.004 0.050 1741 Dihedral : 5.512 56.802 1399 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.67 % Allowed : 16.14 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1172 helix: 2.21 (0.20), residues: 632 sheet: -0.28 (0.55), residues: 86 loop : -1.24 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.003 0.001 HIS B 266 PHE 0.014 0.001 PHE C 121 TYR 0.022 0.001 TYR B 338 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7657 (mt) REVERT: A 425 MET cc_start: 0.6158 (ttm) cc_final: 0.5671 (ttp) REVERT: A 603 GLU cc_start: 0.5504 (OUTLIER) cc_final: 0.5163 (tt0) REVERT: C 67 ASP cc_start: 0.5970 (t0) cc_final: 0.5569 (t0) outliers start: 27 outliers final: 16 residues processed: 126 average time/residue: 0.2493 time to fit residues: 43.5398 Evaluate side-chains 110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 218 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.191101 restraints weight = 10492.856| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.08 r_work: 0.3679 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9830 Z= 0.170 Angle : 0.500 8.637 13292 Z= 0.256 Chirality : 0.040 0.147 1403 Planarity : 0.004 0.049 1741 Dihedral : 5.295 56.089 1399 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.87 % Allowed : 15.94 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1172 helix: 2.27 (0.20), residues: 632 sheet: -0.18 (0.54), residues: 85 loop : -1.24 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.004 0.001 HIS B 266 PHE 0.016 0.001 PHE C 121 TYR 0.023 0.001 TYR B 338 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7541 (mt) REVERT: A 219 GLU cc_start: 0.6581 (mp0) cc_final: 0.6233 (mp0) REVERT: A 425 MET cc_start: 0.6276 (ttm) cc_final: 0.5908 (ttp) REVERT: A 461 MET cc_start: 0.7264 (mpp) cc_final: 0.6977 (mtm) REVERT: A 603 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5422 (tt0) REVERT: C 67 ASP cc_start: 0.5974 (t0) cc_final: 0.5548 (t0) outliers start: 29 outliers final: 23 residues processed: 120 average time/residue: 0.2278 time to fit residues: 38.4695 Evaluate side-chains 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 218 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.213065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.192089 restraints weight = 10549.617| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.03 r_work: 0.3715 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9830 Z= 0.175 Angle : 0.506 8.481 13292 Z= 0.256 Chirality : 0.040 0.144 1403 Planarity : 0.004 0.049 1741 Dihedral : 5.131 55.463 1399 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.87 % Allowed : 16.73 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1172 helix: 2.31 (0.20), residues: 632 sheet: -0.15 (0.55), residues: 85 loop : -1.21 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 129 HIS 0.003 0.001 HIS B 266 PHE 0.016 0.001 PHE C 121 TYR 0.024 0.001 TYR B 338 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7586 (mt) REVERT: A 425 MET cc_start: 0.6394 (ttm) cc_final: 0.6147 (ttp) REVERT: A 461 MET cc_start: 0.7168 (mpp) cc_final: 0.6900 (mtm) REVERT: A 617 TYR cc_start: 0.8613 (m-80) cc_final: 0.8133 (m-80) REVERT: C 67 ASP cc_start: 0.6134 (t0) cc_final: 0.5707 (t0) outliers start: 29 outliers final: 20 residues processed: 119 average time/residue: 0.2688 time to fit residues: 45.1122 Evaluate side-chains 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.4980 chunk 19 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 487 GLN A 576 GLN B 218 ASN B 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.214950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.195910 restraints weight = 10626.449| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.05 r_work: 0.3773 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9830 Z= 0.142 Angle : 0.486 8.355 13292 Z= 0.248 Chirality : 0.039 0.137 1403 Planarity : 0.004 0.048 1741 Dihedral : 4.776 52.925 1399 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.28 % Allowed : 17.52 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1172 helix: 2.38 (0.20), residues: 632 sheet: 0.07 (0.56), residues: 83 loop : -1.16 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.002 0.000 HIS B 266 PHE 0.013 0.001 PHE C 121 TYR 0.023 0.001 TYR B 338 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7231 (mp0) cc_final: 0.6753 (mp0) REVERT: A 219 GLU cc_start: 0.6471 (mp0) cc_final: 0.6146 (mp0) REVERT: A 259 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6830 (mt-10) REVERT: A 461 MET cc_start: 0.7199 (mpp) cc_final: 0.6943 (mtm) REVERT: A 617 TYR cc_start: 0.8556 (m-80) cc_final: 0.8027 (m-80) REVERT: B 338 TYR cc_start: 0.7833 (m-80) cc_final: 0.7323 (m-10) REVERT: C 67 ASP cc_start: 0.6089 (t0) cc_final: 0.5718 (t0) outliers start: 23 outliers final: 16 residues processed: 115 average time/residue: 0.3084 time to fit residues: 51.3676 Evaluate side-chains 106 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.211840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.193021 restraints weight = 10742.456| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.01 r_work: 0.3687 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9830 Z= 0.249 Angle : 0.532 8.315 13292 Z= 0.274 Chirality : 0.041 0.146 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.844 53.406 1399 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.77 % Allowed : 17.03 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1172 helix: 2.27 (0.21), residues: 631 sheet: -0.09 (0.55), residues: 85 loop : -1.25 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 105 HIS 0.005 0.001 HIS B 266 PHE 0.020 0.001 PHE C 121 TYR 0.022 0.001 TYR B 338 ARG 0.004 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7371 (mt) REVERT: A 219 GLU cc_start: 0.6482 (mp0) cc_final: 0.6082 (mp0) REVERT: A 259 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6750 (mt-10) REVERT: A 461 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6898 (mtm) REVERT: B 184 ASN cc_start: 0.6993 (m110) cc_final: 0.6598 (m110) REVERT: B 334 ASN cc_start: 0.7598 (m-40) cc_final: 0.7213 (m-40) REVERT: C 67 ASP cc_start: 0.6065 (t0) cc_final: 0.5658 (t0) outliers start: 28 outliers final: 21 residues processed: 124 average time/residue: 0.2397 time to fit residues: 41.7055 Evaluate side-chains 119 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.0030 chunk 112 optimal weight: 0.7980 overall best weight: 0.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 487 GLN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.213175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.190995 restraints weight = 10514.550| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.15 r_work: 0.3711 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9830 Z= 0.133 Angle : 0.484 8.318 13292 Z= 0.248 Chirality : 0.039 0.134 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.435 48.436 1399 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.28 % Allowed : 17.33 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1172 helix: 2.38 (0.20), residues: 632 sheet: 0.01 (0.55), residues: 81 loop : -1.17 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.002 0.000 HIS A 565 PHE 0.011 0.001 PHE C 121 TYR 0.024 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7460 (mt) REVERT: A 219 GLU cc_start: 0.6508 (mp0) cc_final: 0.6272 (mp0) REVERT: A 259 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6852 (mt-10) REVERT: A 461 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7019 (mtm) REVERT: A 617 TYR cc_start: 0.8603 (m-80) cc_final: 0.8091 (m-80) REVERT: C 67 ASP cc_start: 0.6250 (t0) cc_final: 0.5813 (t0) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.2527 time to fit residues: 41.0978 Evaluate side-chains 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.2980 chunk 114 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 487 GLN B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.211379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.188361 restraints weight = 10670.498| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.19 r_work: 0.3719 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9830 Z= 0.173 Angle : 0.498 8.296 13292 Z= 0.256 Chirality : 0.040 0.161 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.360 46.853 1399 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.18 % Allowed : 17.62 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1172 helix: 2.37 (0.20), residues: 632 sheet: 0.09 (0.55), residues: 85 loop : -1.16 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 129 HIS 0.003 0.001 HIS B 266 PHE 0.016 0.001 PHE C 121 TYR 0.032 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7482 (mt) REVERT: A 259 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6836 (mt-10) REVERT: A 461 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7041 (mtm) REVERT: C 67 ASP cc_start: 0.6319 (t0) cc_final: 0.5864 (t0) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.2393 time to fit residues: 36.8830 Evaluate side-chains 109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.0020 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.213868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.198972 restraints weight = 10606.696| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 0.77 r_work: 0.3923 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9830 Z= 0.163 Angle : 0.499 8.279 13292 Z= 0.256 Chirality : 0.040 0.168 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.263 44.836 1399 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.18 % Allowed : 17.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1172 helix: 2.38 (0.20), residues: 632 sheet: 0.22 (0.55), residues: 83 loop : -1.15 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 105 HIS 0.003 0.001 HIS B 266 PHE 0.015 0.001 PHE C 121 TYR 0.030 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4436.64 seconds wall clock time: 80 minutes 50.60 seconds (4850.60 seconds total)