Starting phenix.real_space_refine on Wed Aug 5 02:07:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s67_54623/08_2026/9s67_54623.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s67_54623/08_2026/9s67_54623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s67_54623/08_2026/9s67_54623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s67_54623/08_2026/9s67_54623.map" model { file = "/net/cci-nas-00/data/ceres_data/9s67_54623/08_2026/9s67_54623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s67_54623/08_2026/9s67_54623.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 5024 2.51 5 N 1303 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7889 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1643 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1677 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "C" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4457 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 38, 'TRANS': 521} Chain breaks: 1 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 1.79, per 1000 atoms: 0.23 Number of scatterers: 7889 At special positions: 0 Unit cell: (75.6, 120.96, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1533 8.00 N 1303 7.00 C 5024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " 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 C1301 " - " ASN C 66 " " NAG C1302 " - " ASN C 110 " " NAG C1303 " - " ASN C 145 " " NAG C1304 " - " ASN C 228 " " NAG C1305 " - " ASN C 319 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 358 " " NAG C1308 " - " ASN C 120 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 386.6 milliseconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 17 sheets defined 8.4% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.840A pdb=" N SER A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 removed outlier: 3.552A pdb=" N HIS A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.075A pdb=" N VAL C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.511A pdb=" N TRP C 341 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.576A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 391 through 398 removed outlier: 4.025A pdb=" N VAL C 395 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 398 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.593A pdb=" N ASN C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.818A pdb=" N GLN C 493 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.839A pdb=" N ASP A 104 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.786A pdb=" N TYR A 49 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU A 46 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN A 37 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 90 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 96 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 117 removed outlier: 5.933A pdb=" N TYR A 172 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 8 Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.642A pdb=" N LEU B 12 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 131 through 135 removed outlier: 6.269A pdb=" N TYR B 187 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 143 removed outlier: 6.269A pdb=" N TYR B 187 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 180 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 165 removed outlier: 4.765A pdb=" N TYR B 205 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 60 removed outlier: 3.573A pdb=" N LYS C 266 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 68 through 71 removed outlier: 4.040A pdb=" N LYS C 181 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C 223 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 197 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE C 221 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 199 " --> pdb=" O PRO C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.943A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 149 removed outlier: 4.258A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 313 through 316 removed outlier: 6.657A pdb=" N VAL C 314 " --> pdb=" O ASN C 529 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY C 553 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.940A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN C 382 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 503 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 384 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 501 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 499 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C 496 " --> pdb=" O TRP C 424 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP C 424 " --> pdb=" O ARG C 496 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 423 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 342 through 346 removed outlier: 3.940A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C 511 " --> pdb=" O PHE C 380 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.86 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: 2487 1.34 - 1.46: 2052 1.46 - 1.58: 3526 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 8098 Sorted by residual: bond pdb=" CB TRP B 36 " pdb=" CG TRP B 36 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.61e-01 bond pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.10e-02 8.26e+03 6.43e-01 bond pdb=" N THR C 360 " pdb=" CA THR C 360 " ideal model delta sigma weight residual 1.463 1.454 0.009 1.08e-02 8.57e+03 6.40e-01 bond pdb=" CB TRP B 47 " pdb=" CG TRP B 47 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.36e-01 bond pdb=" CB GLN B 6 " pdb=" CG GLN B 6 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.23e-01 ... (remaining 8093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 10588 1.10 - 2.21: 337 2.21 - 3.31: 85 3.31 - 4.41: 13 4.41 - 5.52: 7 Bond angle restraints: 11030 Sorted by residual: angle pdb=" N ILE C 456 " pdb=" CA ILE C 456 " pdb=" C ILE C 456 " ideal model delta sigma weight residual 113.20 109.64 3.56 9.60e-01 1.09e+00 1.38e+01 angle pdb=" N GLY C 101 " pdb=" CA GLY C 101 " pdb=" C GLY C 101 " ideal model delta sigma weight residual 110.38 114.97 -4.59 1.28e+00 6.10e-01 1.29e+01 angle pdb=" N VAL C 355 " pdb=" CA VAL C 355 " pdb=" C VAL C 355 " ideal model delta sigma weight residual 112.80 109.09 3.71 1.15e+00 7.56e-01 1.04e+01 angle pdb=" C ARG A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.76e+00 angle pdb=" C SER A 30 " pdb=" CA SER A 30 " pdb=" CB SER A 30 " ideal model delta sigma weight residual 110.42 115.94 -5.52 1.99e+00 2.53e-01 7.68e+00 ... (remaining 11025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.15: 4498 13.15 - 26.29: 293 26.29 - 39.44: 80 39.44 - 52.58: 28 52.58 - 65.73: 9 Dihedral angle restraints: 4908 sinusoidal: 2013 harmonic: 2895 Sorted by residual: dihedral pdb=" CA ILE B 51 " pdb=" C ILE B 51 " pdb=" N ASN B 52 " pdb=" CA ASN B 52 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA GLU B 50 " pdb=" C GLU B 50 " pdb=" N ILE B 51 " pdb=" CA ILE B 51 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASN B 52 " pdb=" C ASN B 52 " pdb=" N HIS B 53 " pdb=" CA HIS B 53 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 765 0.031 - 0.063: 301 0.063 - 0.094: 93 0.094 - 0.125: 72 0.125 - 0.156: 8 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 358 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE C 149 " pdb=" N ILE C 149 " pdb=" C ILE C 149 " pdb=" CB ILE C 149 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE C 117 " pdb=" N ILE C 117 " pdb=" C ILE C 117 " pdb=" CB ILE C 117 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1236 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 159 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 160 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 507 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO C 508 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 508 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 508 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 13 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO B 14 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.022 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 4514 3.02 - 3.49: 7264 3.49 - 3.96: 11688 3.96 - 4.43: 12718 4.43 - 4.90: 21561 Nonbonded interactions: 57745 Sorted by model distance: nonbonded pdb=" CA ASN C 51 " pdb=" O TYR C 267 " model vdw 2.547 2.776 nonbonded pdb=" O LEU C 142 " pdb=" CA ASN C 146 " model vdw 2.604 2.776 nonbonded pdb=" N VAL C 355 " pdb=" N LEU C 356 " model vdw 2.604 2.560 nonbonded pdb=" N ILE A 75 " pdb=" CG1 ILE A 75 " model vdw 2.607 2.816 nonbonded pdb=" N LEU B 149 " pdb=" O LEU B 149 " model vdw 2.613 2.496 ... (remaining 57740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8117 Z= 0.128 Angle : 0.526 5.515 11076 Z= 0.283 Chirality : 0.043 0.156 1239 Planarity : 0.004 0.046 1416 Dihedral : 10.288 65.731 3019 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.17 % Allowed : 6.51 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.26), residues: 989 helix: -1.54 (0.95), residues: 33 sheet: 0.32 (0.28), residues: 357 loop : -1.17 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.013 0.001 TYR B 94 PHE 0.008 0.001 PHE C 528 TRP 0.008 0.001 TRP A 147 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8098) covalent geometry : angle 0.52008 / 0.28 (11030) SS BOND : bond 0.00401 / 0.23 ( 11) SS BOND : angle 0.85322 / 0.55 ( 22) hydrogen bonds : bond 0.12785 / 8.37 ( 230) hydrogen bonds : angle 6.57172 / 4.33 ( 612) link_NAG-ASN : bond 0.00237 / 0.12 ( 8) link_NAG-ASN : angle 1.66951 / 1.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7735 (t) cc_final: 0.7445 (p) REVERT: A 141 ARG cc_start: 0.7237 (tpt90) cc_final: 0.7029 (tmt170) REVERT: A 209 ASN cc_start: 0.6425 (t0) cc_final: 0.5801 (t0) REVERT: B 210 ASN cc_start: 0.8505 (t0) cc_final: 0.8219 (t0) REVERT: C 90 PHE cc_start: 0.8145 (t80) cc_final: 0.7933 (t80) REVERT: C 170 ASN cc_start: 0.7049 (t0) cc_final: 0.6730 (t0) REVERT: C 371 SER cc_start: 0.8902 (t) cc_final: 0.8636 (m) REVERT: C 558 ASP cc_start: 0.6532 (m-30) cc_final: 0.5820 (m-30) REVERT: C 559 PHE cc_start: 0.5675 (m-10) cc_final: 0.5401 (m-80) outliers start: 19 outliers final: 15 residues processed: 156 average time/residue: 0.1026 time to fit residues: 21.0781 Evaluate side-chains 107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0010 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.219577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200324 restraints weight = 11061.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.195818 restraints weight = 16453.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.194685 restraints weight = 16966.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.195082 restraints weight = 16945.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.194651 restraints weight = 12714.381| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8117 Z= 0.144 Angle : 0.589 8.242 11076 Z= 0.306 Chirality : 0.046 0.215 1239 Planarity : 0.005 0.062 1416 Dihedral : 5.311 59.602 1245 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.26), residues: 989 helix: -1.33 (0.84), residues: 43 sheet: 0.40 (0.28), residues: 351 loop : -1.24 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 50 TYR 0.039 0.002 TYR C 441 PHE 0.016 0.001 PHE C 530 TRP 0.010 0.001 TRP A 147 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8098) covalent geometry : angle 0.58144 / 0.30 (11030) SS BOND : bond 0.00456 / 0.27 ( 11) SS BOND : angle 1.30519 / 0.92 ( 22) hydrogen bonds : bond 0.03403 / 2.28 ( 230) hydrogen bonds : angle 5.85426 / 3.89 ( 612) link_NAG-ASN : bond 0.00298 / 0.15 ( 8) link_NAG-ASN : angle 1.77678 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7638 (t) cc_final: 0.7380 (p) REVERT: A 135 LEU cc_start: 0.8119 (mm) cc_final: 0.7657 (mp) REVERT: A 209 ASN cc_start: 0.6059 (t0) cc_final: 0.5643 (t0) REVERT: B 20 LEU cc_start: 0.7476 (mt) cc_final: 0.6952 (mp) REVERT: B 208 ASN cc_start: 0.7822 (m-40) cc_final: 0.7269 (m-40) REVERT: B 210 ASN cc_start: 0.8431 (t0) cc_final: 0.8223 (t0) REVERT: C 90 PHE cc_start: 0.8049 (t80) cc_final: 0.7845 (t80) REVERT: C 170 ASN cc_start: 0.6997 (t0) cc_final: 0.6639 (t0) REVERT: C 371 SER cc_start: 0.9006 (t) cc_final: 0.8772 (m) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.0964 time to fit residues: 16.6438 Evaluate side-chains 93 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.225781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.207164 restraints weight = 11318.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.203885 restraints weight = 15297.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201527 restraints weight = 12446.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.199902 restraints weight = 13525.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198269 restraints weight = 14131.180| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8117 Z= 0.134 Angle : 0.576 7.929 11076 Z= 0.299 Chirality : 0.045 0.190 1239 Planarity : 0.004 0.043 1416 Dihedral : 5.231 55.708 1245 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.26), residues: 989 helix: -1.52 (0.79), residues: 43 sheet: 0.39 (0.28), residues: 351 loop : -1.29 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.035 0.002 TYR C 441 PHE 0.016 0.001 PHE C 263 TRP 0.021 0.002 TRP A 32 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 8098) covalent geometry : angle 0.56733 / 0.30 (11030) SS BOND : bond 0.00455 / 0.27 ( 11) SS BOND : angle 1.50460 / 1.04 ( 22) hydrogen bonds : bond 0.03451 / 2.34 ( 230) hydrogen bonds : angle 5.79658 / 3.85 ( 612) link_NAG-ASN : bond 0.00455 / 0.24 ( 8) link_NAG-ASN : angle 1.76929 / 1.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TRP cc_start: 0.7841 (m100) cc_final: 0.5992 (m100) REVERT: A 56 SER cc_start: 0.7574 (t) cc_final: 0.7310 (p) REVERT: A 124 LEU cc_start: 0.8599 (mt) cc_final: 0.8392 (mt) REVERT: B 6 GLN cc_start: 0.8119 (pm20) cc_final: 0.7524 (pt0) REVERT: B 208 ASN cc_start: 0.7795 (m-40) cc_final: 0.7224 (m-40) REVERT: C 39 ARG cc_start: 0.7107 (mmt180) cc_final: 0.6627 (mmm160) REVERT: C 90 PHE cc_start: 0.8069 (t80) cc_final: 0.7829 (t80) REVERT: C 170 ASN cc_start: 0.6992 (t0) cc_final: 0.6648 (t0) REVERT: C 371 SER cc_start: 0.8862 (t) cc_final: 0.8636 (m) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0956 time to fit residues: 15.1751 Evaluate side-chains 89 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.221345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.201979 restraints weight = 11433.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.199075 restraints weight = 15772.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.196420 restraints weight = 12276.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.194300 restraints weight = 14941.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.193106 restraints weight = 14223.590| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8117 Z= 0.228 Angle : 0.640 5.876 11076 Z= 0.336 Chirality : 0.047 0.175 1239 Planarity : 0.005 0.043 1416 Dihedral : 5.564 55.066 1245 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 989 helix: -1.64 (0.79), residues: 43 sheet: 0.09 (0.28), residues: 362 loop : -1.34 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 221 TYR 0.039 0.002 TYR A 91 PHE 0.018 0.002 PHE C 530 TRP 0.030 0.002 TRP A 32 HIS 0.008 0.002 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 ( 8098) covalent geometry : angle 0.62993 / 0.33 (11030) SS BOND : bond 0.00618 / 0.35 ( 11) SS BOND : angle 1.69981 / 1.19 ( 22) hydrogen bonds : bond 0.04138 / 2.83 ( 230) hydrogen bonds : angle 6.15216 / 4.07 ( 612) link_NAG-ASN : bond 0.00345 / 0.18 ( 8) link_NAG-ASN : angle 2.06607 / 1.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7596 (t) cc_final: 0.7322 (p) REVERT: A 124 LEU cc_start: 0.8636 (mt) cc_final: 0.8376 (mt) REVERT: A 147 TRP cc_start: 0.2288 (m-10) cc_final: 0.2032 (m-10) REVERT: A 209 ASN cc_start: 0.6162 (t0) cc_final: 0.5956 (t0) REVERT: B 208 ASN cc_start: 0.7832 (m-40) cc_final: 0.7386 (m-40) REVERT: C 90 PHE cc_start: 0.8182 (t80) cc_final: 0.7942 (t80) REVERT: C 170 ASN cc_start: 0.7020 (t0) cc_final: 0.6733 (t0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0868 time to fit residues: 13.4646 Evaluate side-chains 92 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 HIS C 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.225604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.205791 restraints weight = 11343.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.202826 restraints weight = 16216.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201837 restraints weight = 13060.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.201401 restraints weight = 14626.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.200643 restraints weight = 11844.844| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8117 Z= 0.139 Angle : 0.579 5.696 11076 Z= 0.298 Chirality : 0.046 0.203 1239 Planarity : 0.004 0.043 1416 Dihedral : 5.359 54.603 1245 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.26), residues: 989 helix: -1.67 (0.82), residues: 38 sheet: 0.25 (0.28), residues: 352 loop : -1.29 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.029 0.001 TYR A 91 PHE 0.012 0.001 PHE C 559 TRP 0.020 0.002 TRP A 32 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8098) covalent geometry : angle 0.56731 / 0.30 (11030) SS BOND : bond 0.00442 / 0.24 ( 11) SS BOND : angle 1.36505 / 1.00 ( 22) hydrogen bonds : bond 0.03446 / 2.39 ( 230) hydrogen bonds : angle 5.88262 / 3.89 ( 612) link_NAG-ASN : bond 0.00494 / 0.26 ( 8) link_NAG-ASN : angle 2.27103 / 1.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7604 (t) cc_final: 0.7308 (p) REVERT: A 124 LEU cc_start: 0.8635 (mt) cc_final: 0.8246 (mt) REVERT: A 209 ASN cc_start: 0.6259 (t0) cc_final: 0.6031 (t0) REVERT: B 208 ASN cc_start: 0.7847 (m-40) cc_final: 0.7408 (m-40) REVERT: C 90 PHE cc_start: 0.8143 (t80) cc_final: 0.7881 (t80) REVERT: C 371 SER cc_start: 0.8876 (t) cc_final: 0.8610 (m) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0944 time to fit residues: 14.7898 Evaluate side-chains 90 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.207633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.203048 restraints weight = 10236.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.202074 restraints weight = 17775.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.201725 restraints weight = 18339.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.183290 restraints weight = 17179.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.177176 restraints weight = 22018.814| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8117 Z= 0.140 Angle : 0.581 5.776 11076 Z= 0.300 Chirality : 0.045 0.152 1239 Planarity : 0.004 0.044 1416 Dihedral : 5.243 54.288 1245 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.27), residues: 989 helix: -1.54 (0.88), residues: 38 sheet: 0.16 (0.28), residues: 360 loop : -1.29 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.027 0.001 TYR A 91 PHE 0.018 0.001 PHE C 263 TRP 0.018 0.002 TRP A 32 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8098) covalent geometry : angle 0.56880 / 0.30 (11030) SS BOND : bond 0.00487 / 0.27 ( 11) SS BOND : angle 1.63857 / 1.14 ( 22) hydrogen bonds : bond 0.03455 / 2.35 ( 230) hydrogen bonds : angle 5.77454 / 3.81 ( 612) link_NAG-ASN : bond 0.00403 / 0.21 ( 8) link_NAG-ASN : angle 2.20960 / 1.41 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7831 (t) cc_final: 0.7554 (p) REVERT: A 209 ASN cc_start: 0.7125 (t0) cc_final: 0.6701 (t0) REVERT: C 39 ARG cc_start: 0.7123 (mmt180) cc_final: 0.6477 (mmt180) REVERT: C 90 PHE cc_start: 0.8243 (t80) cc_final: 0.7979 (t80) REVERT: C 185 GLU cc_start: 0.6188 (mt-10) cc_final: 0.5742 (mt-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0926 time to fit residues: 13.3997 Evaluate side-chains 88 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN C 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.220682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.200524 restraints weight = 11453.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196981 restraints weight = 17807.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.195712 restraints weight = 17149.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.193736 restraints weight = 16351.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.192756 restraints weight = 16911.078| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8117 Z= 0.238 Angle : 0.667 5.920 11076 Z= 0.349 Chirality : 0.047 0.159 1239 Planarity : 0.005 0.043 1416 Dihedral : 5.671 53.810 1245 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.11 % Allowed : 1.60 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.26), residues: 989 helix: -1.66 (0.86), residues: 38 sheet: -0.01 (0.28), residues: 361 loop : -1.45 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 97 TYR 0.041 0.002 TYR A 91 PHE 0.016 0.002 PHE C 530 TRP 0.029 0.003 TRP A 32 HIS 0.008 0.002 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 ( 8098) covalent geometry : angle 0.65227 / 0.34 (11030) SS BOND : bond 0.00605 / 0.34 ( 11) SS BOND : angle 2.09211 / 1.45 ( 22) hydrogen bonds : bond 0.04413 / 3.02 ( 230) hydrogen bonds : angle 6.13033 / 4.04 ( 612) link_NAG-ASN : bond 0.00291 / 0.15 ( 8) link_NAG-ASN : angle 2.46353 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7696 (t) cc_final: 0.7372 (p) REVERT: A 209 ASN cc_start: 0.6570 (t0) cc_final: 0.6249 (t0) REVERT: C 170 ASN cc_start: 0.6819 (t0) cc_final: 0.6549 (t0) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.0918 time to fit residues: 14.3434 Evaluate side-chains 88 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.223541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203484 restraints weight = 11384.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.199827 restraints weight = 17298.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.197746 restraints weight = 17411.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.196928 restraints weight = 16761.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.194199 restraints weight = 15988.388| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8117 Z= 0.144 Angle : 0.599 6.659 11076 Z= 0.308 Chirality : 0.046 0.149 1239 Planarity : 0.005 0.044 1416 Dihedral : 5.391 53.932 1245 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.26), residues: 989 helix: -1.75 (0.84), residues: 38 sheet: 0.13 (0.28), residues: 360 loop : -1.39 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 97 TYR 0.026 0.001 TYR A 91 PHE 0.013 0.001 PHE C 263 TRP 0.019 0.002 TRP A 32 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 8098) covalent geometry : angle 0.58649 / 0.30 (11030) SS BOND : bond 0.00430 / 0.23 ( 11) SS BOND : angle 1.70869 / 1.24 ( 22) hydrogen bonds : bond 0.03509 / 2.41 ( 230) hydrogen bonds : angle 5.88498 / 3.88 ( 612) link_NAG-ASN : bond 0.00399 / 0.21 ( 8) link_NAG-ASN : angle 2.21751 / 1.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7652 (t) cc_final: 0.7301 (p) REVERT: A 135 LEU cc_start: 0.8116 (mm) cc_final: 0.7619 (mp) REVERT: A 209 ASN cc_start: 0.6651 (t0) cc_final: 0.6194 (t0) REVERT: C 39 ARG cc_start: 0.6983 (mmt180) cc_final: 0.6603 (tpm170) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0983 time to fit residues: 14.2644 Evaluate side-chains 85 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN B 182 GLN C 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.222294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.202891 restraints weight = 11317.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200646 restraints weight = 17068.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.197469 restraints weight = 12516.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194346 restraints weight = 12543.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.192610 restraints weight = 14097.293| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8117 Z= 0.173 Angle : 0.625 8.008 11076 Z= 0.323 Chirality : 0.046 0.148 1239 Planarity : 0.005 0.044 1416 Dihedral : 5.456 53.648 1245 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.11 % Allowed : 0.23 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.26), residues: 989 helix: -1.77 (0.83), residues: 38 sheet: 0.07 (0.28), residues: 361 loop : -1.43 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.030 0.001 TYR A 91 PHE 0.015 0.001 PHE C 559 TRP 0.021 0.002 TRP A 32 HIS 0.007 0.002 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 8098) covalent geometry : angle 0.61158 / 0.32 (11030) SS BOND : bond 0.00500 / 0.27 ( 11) SS BOND : angle 1.83833 / 1.32 ( 22) hydrogen bonds : bond 0.03746 / 2.56 ( 230) hydrogen bonds : angle 5.88596 / 3.89 ( 612) link_NAG-ASN : bond 0.00341 / 0.18 ( 8) link_NAG-ASN : angle 2.23779 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 SER cc_start: 0.7537 (t) cc_final: 0.7184 (p) REVERT: A 135 LEU cc_start: 0.8138 (mm) cc_final: 0.7647 (mp) REVERT: A 209 ASN cc_start: 0.6917 (t0) cc_final: 0.6238 (t0) REVERT: C 39 ARG cc_start: 0.7003 (mmt180) cc_final: 0.6611 (tpm170) REVERT: C 170 ASN cc_start: 0.6983 (t0) cc_final: 0.6666 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0907 time to fit residues: 13.2174 Evaluate side-chains 83 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 0.0670 chunk 67 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 0.0970 chunk 83 optimal weight: 0.3980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN C 54 HIS ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.225875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.206615 restraints weight = 11393.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.202740 restraints weight = 16293.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201133 restraints weight = 16917.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200935 restraints weight = 13402.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.199267 restraints weight = 12732.068| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8117 Z= 0.108 Angle : 0.581 7.264 11076 Z= 0.295 Chirality : 0.045 0.144 1239 Planarity : 0.005 0.045 1416 Dihedral : 5.141 53.751 1245 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 989 helix: -1.75 (0.83), residues: 38 sheet: 0.34 (0.28), residues: 349 loop : -1.48 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.018 0.001 TYR A 91 PHE 0.012 0.001 PHE C 263 TRP 0.012 0.001 TRP A 32 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8098) covalent geometry : angle 0.57079 / 0.29 (11030) SS BOND : bond 0.00335 / 0.18 ( 11) SS BOND : angle 1.49404 / 1.11 ( 22) hydrogen bonds : bond 0.03074 / 2.08 ( 230) hydrogen bonds : angle 5.57810 / 3.69 ( 612) link_NAG-ASN : bond 0.00431 / 0.22 ( 8) link_NAG-ASN : angle 1.99588 / 1.35 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LEU cc_start: 0.8519 (mt) cc_final: 0.8313 (mt) REVERT: A 135 LEU cc_start: 0.8008 (mm) cc_final: 0.7534 (mp) REVERT: A 209 ASN cc_start: 0.6473 (t0) cc_final: 0.5949 (t0) REVERT: C 39 ARG cc_start: 0.6781 (mmt180) cc_final: 0.6352 (tpm170) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1049 time to fit residues: 14.2999 Evaluate side-chains 81 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.224097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.203171 restraints weight = 11316.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.199647 restraints weight = 16464.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.198349 restraints weight = 15902.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.197927 restraints weight = 17334.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.196917 restraints weight = 14680.186| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8117 Z= 0.131 Angle : 0.591 7.091 11076 Z= 0.302 Chirality : 0.045 0.144 1239 Planarity : 0.005 0.044 1416 Dihedral : 5.182 53.425 1245 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.26), residues: 989 helix: -1.78 (0.82), residues: 38 sheet: 0.33 (0.28), residues: 350 loop : -1.47 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 189 TYR 0.024 0.001 TYR A 91 PHE 0.015 0.001 PHE C 559 TRP 0.016 0.001 TRP A 32 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8098) covalent geometry : angle 0.58033 / 0.30 (11030) SS BOND : bond 0.00355 / 0.19 ( 11) SS BOND : angle 1.50344 / 1.09 ( 22) hydrogen bonds : bond 0.03304 / 2.24 ( 230) hydrogen bonds : angle 5.59044 / 3.69 ( 612) link_NAG-ASN : bond 0.00353 / 0.18 ( 8) link_NAG-ASN : angle 2.03337 / 1.40 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.35 seconds wall clock time: 21 minutes 21.83 seconds (1281.83 seconds total)