Starting phenix.real_space_refine on Tue May 13 00:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0f_36763/05_2025/8k0f_36763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0f_36763/05_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_36763/05_2025/8k0f_36763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0f_36763/05_2025/8k0f_36763.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0f_36763/05_2025/8k0f_36763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0f_36763/05_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-5687/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: 5.82, per 1000 atoms: 0.61 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 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: 0.98 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: 2.76 Time building geometry restraints manager: 2.71 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: 0.720 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- 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 9837 Z= 0.162 Angle : 0.631 13.032 13310 Z= 0.337 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 4) link_NAG-ASN : angle 3.14326 ( 12) hydrogen bonds : bond 0.16534 ( 505) hydrogen bonds : angle 5.85543 ( 1581) SS BOND : bond 0.00197 ( 3) SS BOND : angle 3.37621 ( 6) covalent geometry : bond 0.00419 ( 9830) covalent geometry : angle 0.62006 (13292) *********************** 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 : 1.025 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: 0.2516 time to fit residues: 34.6830 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 : 1.083 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.0000 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 = 0.186780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153666 restraints weight = 10147.778| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.87 r_work: 0.3310 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 9837 Z= 0.111 Angle : 0.547 11.125 13310 Z= 0.271 Chirality : 0.040 0.282 1403 Planarity : 0.004 0.048 1741 Dihedral : 7.567 84.061 1399 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 2.07 (0.21), residues: 628 sheet: -0.42 (0.54), residues: 87 loop : -1.27 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.003 0.001 HIS C 62 PHE 0.014 0.001 PHE C 121 TYR 0.020 0.001 TYR B 338 ARG 0.004 0.000 ARG A 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 4) link_NAG-ASN : angle 2.24310 ( 12) hydrogen bonds : bond 0.04530 ( 505) hydrogen bonds : angle 3.83579 ( 1581) SS BOND : bond 0.00237 ( 3) SS BOND : angle 2.98496 ( 6) covalent geometry : bond 0.00235 ( 9830) covalent geometry : angle 0.53908 (13292) *********************** 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 : 1.029 Fit side-chains REVERT: A 677 THR cc_start: 0.9111 (p) cc_final: 0.7968 (m) REVERT: B 350 GLU cc_start: 0.6419 (mp0) cc_final: 0.6060 (tm-30) outliers start: 22 outliers final: 10 residues processed: 120 average time/residue: 0.2253 time to fit residues: 37.4537 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 : 1.006 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 114 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4233 r_free = 0.4233 target = 0.210145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.187207 restraints weight = 10506.952| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.23 r_work: 0.3610 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9837 Z= 0.136 Angle : 0.534 9.775 13310 Z= 0.271 Chirality : 0.041 0.199 1403 Planarity : 0.004 0.050 1741 Dihedral : 6.283 65.583 1399 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.18 % Allowed : 15.54 % Favored : 82.28 % 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: 1.09 (0.25), residues: 1172 helix: 2.20 (0.21), residues: 629 sheet: -0.31 (0.54), residues: 87 loop : -1.25 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.006 0.001 HIS B 266 PHE 0.017 0.001 PHE C 121 TYR 0.022 0.001 TYR B 338 ARG 0.004 0.000 ARG A 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 4) link_NAG-ASN : angle 2.41235 ( 12) hydrogen bonds : bond 0.05224 ( 505) hydrogen bonds : angle 3.75761 ( 1581) SS BOND : bond 0.00228 ( 3) SS BOND : angle 3.51134 ( 6) covalent geometry : bond 0.00315 ( 9830) covalent geometry : angle 0.52382 (13292) *********************** 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 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 184 ASN cc_start: 0.6856 (m110) cc_final: 0.6635 (m110) REVERT: B 334 ASN cc_start: 0.7683 (m-40) cc_final: 0.7263 (m-40) outliers start: 22 outliers final: 15 residues processed: 122 average time/residue: 0.2177 time to fit residues: 37.2076 Evaluate side-chains 108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 234 GLU 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 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: 3.9990 chunk 116 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 B 218 ASN B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.214017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.193082 restraints weight = 10525.217| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 0.98 r_work: 0.3738 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9837 Z= 0.110 Angle : 0.501 9.199 13310 Z= 0.255 Chirality : 0.039 0.148 1403 Planarity : 0.003 0.049 1741 Dihedral : 5.496 56.740 1399 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.48 % Allowed : 15.94 % Favored : 81.58 % 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: 1.22 (0.25), residues: 1172 helix: 2.30 (0.20), residues: 630 sheet: -0.27 (0.55), residues: 86 loop : -1.18 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 129 HIS 0.004 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 4) link_NAG-ASN : angle 2.50378 ( 12) hydrogen bonds : bond 0.04538 ( 505) hydrogen bonds : angle 3.56160 ( 1581) SS BOND : bond 0.00251 ( 3) SS BOND : angle 3.23167 ( 6) covalent geometry : bond 0.00240 ( 9830) covalent geometry : angle 0.49128 (13292) *********************** 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 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 425 MET cc_start: 0.6293 (ttm) cc_final: 0.6011 (ttp) REVERT: A 603 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.5337 (tt0) outliers start: 25 outliers final: 17 residues processed: 121 average time/residue: 0.2352 time to fit residues: 39.7200 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 : 1.142 ------------------------------------------------------------------------------- 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 277 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 459 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 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 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.211412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.192226 restraints weight = 10484.961| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.03 r_work: 0.3681 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9837 Z= 0.171 Angle : 0.555 8.604 13310 Z= 0.284 Chirality : 0.042 0.154 1403 Planarity : 0.004 0.050 1741 Dihedral : 5.442 56.411 1399 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.07 % Allowed : 15.94 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.25), residues: 1172 helix: 2.22 (0.20), residues: 630 sheet: -0.36 (0.54), residues: 88 loop : -1.26 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.006 0.001 HIS B 266 PHE 0.020 0.002 PHE C 121 TYR 0.024 0.002 TYR B 338 ARG 0.004 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 4) link_NAG-ASN : angle 2.54101 ( 12) hydrogen bonds : bond 0.05808 ( 505) hydrogen bonds : angle 3.75621 ( 1581) SS BOND : bond 0.00298 ( 3) SS BOND : angle 3.60156 ( 6) covalent geometry : bond 0.00411 ( 9830) covalent geometry : angle 0.54486 (13292) *********************** 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 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7425 (mt) REVERT: A 219 GLU cc_start: 0.6478 (mp0) cc_final: 0.6117 (mp0) REVERT: A 259 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6742 (mt-10) REVERT: A 425 MET cc_start: 0.6230 (ttm) cc_final: 0.5976 (ttp) REVERT: B 184 ASN cc_start: 0.6981 (m110) cc_final: 0.6664 (m110) REVERT: B 334 ASN cc_start: 0.7583 (m-40) cc_final: 0.7189 (m-40) outliers start: 31 outliers final: 22 residues processed: 128 average time/residue: 0.2124 time to fit residues: 38.7085 Evaluate side-chains 117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 489 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 B residue 322 LEU Chi-restraints excluded: chain C residue 10 VAL 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: 10.0000 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.209829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.192798 restraints weight = 10527.472| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 0.81 r_work: 0.3761 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9837 Z= 0.177 Angle : 0.566 8.419 13310 Z= 0.291 Chirality : 0.042 0.153 1403 Planarity : 0.004 0.051 1741 Dihedral : 5.350 56.454 1399 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.17 % Allowed : 15.94 % Favored : 80.89 % 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: 1.00 (0.25), residues: 1172 helix: 2.12 (0.20), residues: 630 sheet: -0.29 (0.54), residues: 87 loop : -1.30 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 129 HIS 0.007 0.001 HIS B 266 PHE 0.020 0.002 PHE C 121 TYR 0.025 0.002 TYR B 338 ARG 0.004 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 2.57697 ( 12) hydrogen bonds : bond 0.06100 ( 505) hydrogen bonds : angle 3.80257 ( 1581) SS BOND : bond 0.00384 ( 3) SS BOND : angle 3.83885 ( 6) covalent geometry : bond 0.00428 ( 9830) covalent geometry : angle 0.55491 (13292) *********************** 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 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8283 (mmt) cc_final: 0.7832 (mmt) REVERT: A 68 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7612 (mt) REVERT: A 234 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 259 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6965 (mt-10) REVERT: A 425 MET cc_start: 0.6328 (ttm) cc_final: 0.5886 (ttp) REVERT: B 184 ASN cc_start: 0.6916 (m110) cc_final: 0.6472 (m110) outliers start: 32 outliers final: 25 residues processed: 127 average time/residue: 0.2426 time to fit residues: 42.7505 Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 76 ARG 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 234 GLU Chi-restraints excluded: chain A residue 277 ASN 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 489 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 B residue 322 LEU Chi-restraints excluded: chain C residue 10 VAL 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: 0.6980 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 668 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.211783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.191225 restraints weight = 10608.581| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 0.99 r_work: 0.3770 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9837 Z= 0.116 Angle : 0.511 8.280 13310 Z= 0.262 Chirality : 0.039 0.143 1403 Planarity : 0.004 0.050 1741 Dihedral : 5.025 55.474 1399 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.67 % Allowed : 16.44 % Favored : 80.89 % 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: 1.23 (0.25), residues: 1172 helix: 2.31 (0.20), residues: 629 sheet: -0.26 (0.54), residues: 83 loop : -1.16 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.002 0.001 HIS A 565 PHE 0.014 0.001 PHE C 121 TYR 0.024 0.001 TYR B 338 ARG 0.004 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 4) link_NAG-ASN : angle 2.48724 ( 12) hydrogen bonds : bond 0.04777 ( 505) hydrogen bonds : angle 3.61704 ( 1581) SS BOND : bond 0.00228 ( 3) SS BOND : angle 3.34352 ( 6) covalent geometry : bond 0.00253 ( 9830) covalent geometry : angle 0.50081 (13292) *********************** 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 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7476 (mt) REVERT: A 259 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6774 (mt-10) REVERT: B 184 ASN cc_start: 0.6978 (m110) cc_final: 0.6582 (m110) REVERT: B 334 ASN cc_start: 0.7445 (m-40) cc_final: 0.7188 (m-40) REVERT: C 67 ASP cc_start: 0.6266 (t0) cc_final: 0.5737 (t0) outliers start: 27 outliers final: 21 residues processed: 125 average time/residue: 0.2261 time to fit residues: 39.2787 Evaluate side-chains 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 388 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.211869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.190282 restraints weight = 10753.503| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.11 r_work: 0.3721 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9837 Z= 0.123 Angle : 0.516 8.290 13310 Z= 0.264 Chirality : 0.040 0.141 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.902 54.477 1399 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.48 % Allowed : 16.73 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.25), residues: 1172 helix: 2.30 (0.20), residues: 629 sheet: -0.24 (0.54), residues: 84 loop : -1.17 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.003 0.001 HIS B 266 PHE 0.016 0.001 PHE C 121 TYR 0.026 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 4) link_NAG-ASN : angle 2.42720 ( 12) hydrogen bonds : bond 0.04856 ( 505) hydrogen bonds : angle 3.62875 ( 1581) SS BOND : bond 0.00252 ( 3) SS BOND : angle 3.33155 ( 6) covalent geometry : bond 0.00278 ( 9830) covalent geometry : angle 0.50606 (13292) *********************** 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 119 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7522 (mt) REVERT: A 259 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6807 (mt-10) REVERT: A 461 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6722 (mtm) REVERT: B 184 ASN cc_start: 0.6912 (m110) cc_final: 0.6463 (m110) REVERT: B 334 ASN cc_start: 0.7418 (m-40) cc_final: 0.7114 (m-40) REVERT: C 67 ASP cc_start: 0.6455 (t0) cc_final: 0.5844 (t0) outliers start: 25 outliers final: 20 residues processed: 117 average time/residue: 0.2230 time to fit residues: 36.5650 Evaluate side-chains 114 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 40 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.209739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.184773 restraints weight = 10504.400| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.45 r_work: 0.3615 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9837 Z= 0.122 Angle : 0.520 8.324 13310 Z= 0.266 Chirality : 0.040 0.140 1403 Planarity : 0.004 0.054 1741 Dihedral : 4.770 52.835 1399 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.67 % Allowed : 16.63 % Favored : 80.69 % 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: 1.23 (0.25), residues: 1172 helix: 2.30 (0.20), residues: 631 sheet: -0.19 (0.54), residues: 84 loop : -1.18 (0.28), residues: 457 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 0.016 0.001 PHE C 121 TYR 0.033 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 4) link_NAG-ASN : angle 2.36922 ( 12) hydrogen bonds : bond 0.04791 ( 505) hydrogen bonds : angle 3.62928 ( 1581) SS BOND : bond 0.00249 ( 3) SS BOND : angle 3.30364 ( 6) covalent geometry : bond 0.00275 ( 9830) covalent geometry : angle 0.51042 (13292) *********************** 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 121 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7641 (mt) REVERT: A 219 GLU cc_start: 0.6542 (mp0) cc_final: 0.6251 (mp0) REVERT: A 259 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6955 (mt-10) REVERT: A 461 MET cc_start: 0.7262 (mpp) cc_final: 0.6873 (mtm) REVERT: B 184 ASN cc_start: 0.6808 (m110) cc_final: 0.6344 (m110) REVERT: B 334 ASN cc_start: 0.7330 (m-40) cc_final: 0.7047 (m-40) REVERT: C 67 ASP cc_start: 0.6631 (t0) cc_final: 0.5958 (t0) outliers start: 27 outliers final: 22 residues processed: 120 average time/residue: 0.2764 time to fit residues: 47.8206 Evaluate side-chains 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 177 MET 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 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 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: 0.0870 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 116 optimal weight: 0.0060 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 576 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 = 0.4283 r_free = 0.4283 target = 0.215931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.201158 restraints weight = 10795.552| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 0.77 r_work: 0.3942 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9837 Z= 0.099 Angle : 0.494 8.429 13310 Z= 0.252 Chirality : 0.039 0.144 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.383 46.603 1399 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.88 % Allowed : 17.62 % Favored : 80.50 % 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: 1.38 (0.25), residues: 1172 helix: 2.42 (0.20), residues: 630 sheet: 0.04 (0.56), residues: 82 loop : -1.13 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.002 0.000 HIS C 62 PHE 0.011 0.001 PHE C 121 TYR 0.028 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 4) link_NAG-ASN : angle 2.26836 ( 12) hydrogen bonds : bond 0.03803 ( 505) hydrogen bonds : angle 3.49695 ( 1581) SS BOND : bond 0.00204 ( 3) SS BOND : angle 3.03879 ( 6) covalent geometry : bond 0.00205 ( 9830) covalent geometry : angle 0.48566 (13292) ********************** 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 115 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8061 (pttm) cc_final: 0.7844 (mttm) REVERT: A 259 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6729 (mt-10) REVERT: A 461 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6359 (mtm) REVERT: A 677 THR cc_start: 0.8929 (p) cc_final: 0.7754 (m) REVERT: B 338 TYR cc_start: 0.7693 (m-80) cc_final: 0.7280 (m-10) REVERT: C 67 ASP cc_start: 0.6045 (t0) cc_final: 0.5786 (t0) outliers start: 19 outliers final: 15 residues processed: 112 average time/residue: 0.2420 time to fit residues: 37.1919 Evaluate side-chains 109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 299 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 487 GLN 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 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: 5.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.182036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.149274 restraints weight = 10204.098| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.89 r_work: 0.3237 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9837 Z= 0.136 Angle : 0.526 8.352 13310 Z= 0.270 Chirality : 0.040 0.170 1403 Planarity : 0.004 0.055 1741 Dihedral : 4.412 45.976 1399 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.98 % Allowed : 17.43 % Favored : 80.59 % 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: 1.29 (0.25), residues: 1172 helix: 2.34 (0.21), residues: 631 sheet: -0.10 (0.55), residues: 83 loop : -1.15 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 105 HIS 0.004 0.001 HIS B 266 PHE 0.018 0.001 PHE C 121 TYR 0.029 0.001 TYR B 338 ARG 0.005 0.000 ARG B 212 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 4) link_NAG-ASN : angle 2.22929 ( 12) hydrogen bonds : bond 0.05013 ( 505) hydrogen bonds : angle 3.71286 ( 1581) SS BOND : bond 0.00248 ( 3) SS BOND : angle 3.36382 ( 6) covalent geometry : bond 0.00316 ( 9830) covalent geometry : angle 0.51706 (13292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.76 seconds wall clock time: 76 minutes 57.19 seconds (4617.19 seconds total)