Starting phenix.real_space_refine on Tue Mar 3 19:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsl_30837/03_2026/7dsl_30837_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsl_30837/03_2026/7dsl_30837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2026/7dsl_30837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2026/7dsl_30837.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2026/7dsl_30837_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsl_30837/03_2026/7dsl_30837_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 4938 2.51 5 N 1191 2.21 5 O 1365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7522 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 106 Unusual residues: {'HO0': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} Time building chain proxies: 1.85, per 1000 atoms: 0.25 Number of scatterers: 7522 At special positions: 0 Unit cell: (81.525, 83.699, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 1365 8.00 N 1191 7.00 C 4938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.04 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 282.2 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 58.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 206 removed outlier: 3.647A pdb=" N LEU A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.810A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.594A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.243A pdb=" N VAL A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.948A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.505A pdb=" N ILE A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.673A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.603A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.571A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.670A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.832A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.810A pdb=" N GLU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.650A pdb=" N ALA B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 158 removed outlier: 4.909A pdb=" N TYR B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 189 Processing helix chain 'B' and resid 189 through 221 removed outlier: 3.647A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 253 removed outlier: 3.713A pdb=" N ILE B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.988A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 400 through 421 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.526A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.922A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.794A pdb=" N LEU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.570A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.527A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 627 " --> pdb=" O ARG A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 366 393 hydrogen bonds defined for protein. 1128 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: 1.18 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1170 1.31 - 1.43: 2066 1.43 - 1.56: 4401 1.56 - 1.68: 25 1.68 - 1.81: 41 Bond restraints: 7703 Sorted by residual: bond pdb=" C02 HO0 B 601 " pdb=" C07 HO0 B 601 " ideal model delta sigma weight residual 1.508 1.753 -0.245 2.00e-02 2.50e+03 1.51e+02 bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C09 HO0 B 601 " pdb=" C10 HO0 B 601 " ideal model delta sigma weight residual 1.522 1.341 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" CBG Y01 B 602 " pdb=" CBI Y01 B 602 " ideal model delta sigma weight residual 1.537 1.383 0.154 2.00e-02 2.50e+03 5.92e+01 ... (remaining 7698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 10173 3.16 - 6.32: 264 6.32 - 9.48: 41 9.48 - 12.64: 9 12.64 - 15.80: 3 Bond angle restraints: 10490 Sorted by residual: angle pdb=" N SER B 143 " pdb=" CA SER B 143 " pdb=" C SER B 143 " ideal model delta sigma weight residual 113.18 105.23 7.95 1.33e+00 5.65e-01 3.57e+01 angle pdb=" N THR B 71 " pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 109.81 121.94 -12.13 2.21e+00 2.05e-01 3.01e+01 angle pdb=" C03 HO0 B 601 " pdb=" C10 HO0 B 601 " pdb=" C09 HO0 B 601 " ideal model delta sigma weight residual 113.02 128.82 -15.80 3.00e+00 1.11e-01 2.77e+01 angle pdb=" C08 HO0 B 601 " pdb=" C09 HO0 B 601 " pdb=" C10 HO0 B 601 " ideal model delta sigma weight residual 111.81 127.13 -15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" N LEU B 282 " pdb=" CA LEU B 282 " pdb=" C LEU B 282 " ideal model delta sigma weight residual 109.81 120.96 -11.15 2.21e+00 2.05e-01 2.54e+01 ... (remaining 10485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 4531 35.08 - 70.16: 140 70.16 - 105.24: 24 105.24 - 140.32: 34 140.32 - 175.40: 8 Dihedral angle restraints: 4737 sinusoidal: 2057 harmonic: 2680 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -148.65 62.65 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CA LYS B 479 " pdb=" C LYS B 479 " pdb=" N ASN B 480 " pdb=" CA ASN B 480 " ideal model delta harmonic sigma weight residual 180.00 -151.53 -28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PHE B 231 " pdb=" C PHE B 231 " pdb=" N SER B 232 " pdb=" CA SER B 232 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 4734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.187: 1223 1.187 - 2.374: 0 2.374 - 3.562: 0 3.562 - 4.749: 0 4.749 - 5.936: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -3.00 5.94 2.00e-01 2.50e+01 8.81e+02 chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -2.94 5.88 2.00e-01 2.50e+01 8.65e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.68 -5.53 2.00e-01 2.50e+01 7.64e+02 ... (remaining 1230 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO A 619 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 103 " -0.011 2.00e-02 2.50e+03 1.69e-02 5.68e+00 pdb=" CG TYR B 103 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 103 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 103 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 103 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 103 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 103 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 158 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO B 159 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.033 5.00e-02 4.00e+02 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 97 2.62 - 3.19: 6415 3.19 - 3.76: 11313 3.76 - 4.33: 15776 4.33 - 4.90: 25767 Nonbonded interactions: 59368 Sorted by model distance: nonbonded pdb=" O ASP A 408 " pdb=" OG SER A 409 " model vdw 2.055 3.040 nonbonded pdb=" O GLY B 67 " pdb=" OG1 THR B 71 " model vdw 2.214 3.040 nonbonded pdb=" O ILE B 464 " pdb=" OG SER B 467 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 293 " pdb=" OG SER A 297 " model vdw 2.301 3.040 nonbonded pdb=" O PRO B 368 " pdb=" N LEU B 370 " model vdw 2.310 3.120 ... (remaining 59363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.013 0.245 7712 Z= 0.613 Angle : 1.285 15.802 10516 Z= 0.677 Chirality : 0.491 5.936 1233 Planarity : 0.007 0.077 1282 Dihedral : 22.636 175.403 3012 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.86 % Allowed : 9.13 % Favored : 90.01 % Rotamer: Outliers : 1.14 % Allowed : 6.72 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.21), residues: 931 helix: -1.91 (0.18), residues: 495 sheet: -1.27 (0.62), residues: 62 loop : -3.44 (0.24), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 440 TYR 0.040 0.003 TYR B 103 PHE 0.027 0.003 PHE B 351 TRP 0.016 0.002 TRP A 220 HIS 0.005 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.01315 ( 7703) covalent geometry : angle 1.25858 (10490) SS BOND : bond 0.00655 ( 1) SS BOND : angle 4.82668 ( 2) hydrogen bonds : bond 0.20578 ( 393) hydrogen bonds : angle 6.50041 ( 1128) link_BETA1-4 : bond 0.01217 ( 4) link_BETA1-4 : angle 3.87883 ( 12) link_NAG-ASN : bond 0.00453 ( 4) link_NAG-ASN : angle 6.56833 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.296 Fit side-chains REVERT: A 184 TRP cc_start: 0.8239 (m100) cc_final: 0.7926 (m-10) REVERT: A 360 PHE cc_start: 0.9272 (m-80) cc_final: 0.9070 (m-80) REVERT: A 398 ASP cc_start: 0.7910 (p0) cc_final: 0.7294 (t0) REVERT: B 239 ASP cc_start: 0.7670 (t0) cc_final: 0.7257 (p0) REVERT: B 272 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.8159 (ttt-90) REVERT: B 314 ASP cc_start: 0.8169 (m-30) cc_final: 0.7899 (m-30) REVERT: B 365 MET cc_start: 0.9039 (mtt) cc_final: 0.8631 (mtt) REVERT: B 369 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: B 392 ASP cc_start: 0.7849 (t0) cc_final: 0.7476 (t0) REVERT: B 462 PHE cc_start: 0.8259 (t80) cc_final: 0.7983 (t80) outliers start: 9 outliers final: 1 residues processed: 117 average time/residue: 0.5510 time to fit residues: 68.2370 Evaluate side-chains 65 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 GLN Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 353 ASN A 483 GLN B 230 ASN B 261 ASN B 273 ASN B 398 ASN B 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.074675 restraints weight = 13689.999| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.14 r_work: 0.2755 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7712 Z= 0.162 Angle : 1.290 34.515 10516 Z= 0.512 Chirality : 0.109 1.858 1233 Planarity : 0.005 0.059 1282 Dihedral : 22.908 176.504 1370 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.44 % Favored : 93.02 % Rotamer: Outliers : 2.28 % Allowed : 12.04 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.26), residues: 931 helix: 0.13 (0.23), residues: 505 sheet: -1.06 (0.60), residues: 67 loop : -3.03 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 452 TYR 0.011 0.001 TYR B 103 PHE 0.016 0.001 PHE B 351 TRP 0.010 0.001 TRP A 220 HIS 0.008 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7703) covalent geometry : angle 1.27592 (10490) SS BOND : bond 0.00625 ( 1) SS BOND : angle 4.66625 ( 2) hydrogen bonds : bond 0.06257 ( 393) hydrogen bonds : angle 4.68498 ( 1128) link_BETA1-4 : bond 0.00532 ( 4) link_BETA1-4 : angle 2.15902 ( 12) link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 5.28641 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.305 Fit side-chains REVERT: A 184 TRP cc_start: 0.8439 (m100) cc_final: 0.7909 (m-10) REVERT: A 269 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: A 398 ASP cc_start: 0.7964 (p0) cc_final: 0.7336 (t0) REVERT: B 239 ASP cc_start: 0.7705 (t0) cc_final: 0.7182 (p0) REVERT: B 266 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: B 314 ASP cc_start: 0.8238 (m-30) cc_final: 0.7790 (m-30) REVERT: B 365 MET cc_start: 0.9316 (mtt) cc_final: 0.9047 (ttm) REVERT: B 392 ASP cc_start: 0.7967 (t0) cc_final: 0.7663 (t0) REVERT: B 397 ILE cc_start: 0.8956 (pt) cc_final: 0.8734 (pp) REVERT: B 451 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: B 500 MET cc_start: 0.8771 (mtt) cc_final: 0.8395 (mtm) outliers start: 18 outliers final: 7 residues processed: 86 average time/residue: 0.4591 time to fit residues: 42.4431 Evaluate side-chains 72 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.075159 restraints weight = 13565.551| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.10 r_work: 0.2755 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7712 Z= 0.165 Angle : 1.233 33.111 10516 Z= 0.480 Chirality : 0.108 1.859 1233 Planarity : 0.005 0.052 1282 Dihedral : 22.635 178.213 1367 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.98 % Favored : 92.70 % Rotamer: Outliers : 3.04 % Allowed : 12.67 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.71 (0.28), residues: 931 helix: 0.95 (0.23), residues: 501 sheet: -0.81 (0.62), residues: 67 loop : -2.53 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 614 TYR 0.014 0.001 TYR A 629 PHE 0.020 0.001 PHE B 474 TRP 0.011 0.001 TRP A 220 HIS 0.006 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7703) covalent geometry : angle 1.22084 (10490) SS BOND : bond 0.00497 ( 1) SS BOND : angle 2.36676 ( 2) hydrogen bonds : bond 0.05674 ( 393) hydrogen bonds : angle 4.35883 ( 1128) link_BETA1-4 : bond 0.00468 ( 4) link_BETA1-4 : angle 2.18539 ( 12) link_NAG-ASN : bond 0.00316 ( 4) link_NAG-ASN : angle 4.83734 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.285 Fit side-chains REVERT: A 172 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8851 (ptmt) REVERT: A 184 TRP cc_start: 0.8472 (m100) cc_final: 0.7907 (m-10) REVERT: A 269 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: B 239 ASP cc_start: 0.7684 (t0) cc_final: 0.7254 (p0) REVERT: B 266 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: B 314 ASP cc_start: 0.8228 (m-30) cc_final: 0.7905 (m-30) REVERT: B 365 MET cc_start: 0.9332 (mtt) cc_final: 0.9066 (ttm) REVERT: B 392 ASP cc_start: 0.8022 (t0) cc_final: 0.7771 (t0) REVERT: B 397 ILE cc_start: 0.9033 (pt) cc_final: 0.8731 (pp) REVERT: B 421 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7268 (ptm-80) REVERT: B 451 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7642 (m-10) outliers start: 24 outliers final: 11 residues processed: 89 average time/residue: 0.4820 time to fit residues: 45.9991 Evaluate side-chains 73 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.0050 chunk 78 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS B 47 GLN B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.077846 restraints weight = 13743.888| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.15 r_work: 0.2816 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7712 Z= 0.119 Angle : 1.196 33.516 10516 Z= 0.456 Chirality : 0.107 1.800 1233 Planarity : 0.004 0.050 1282 Dihedral : 22.465 178.352 1367 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.77 % Favored : 93.02 % Rotamer: Outliers : 3.30 % Allowed : 14.07 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.28), residues: 931 helix: 1.39 (0.24), residues: 503 sheet: -0.71 (0.62), residues: 67 loop : -2.22 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 210 TYR 0.015 0.001 TYR A 629 PHE 0.013 0.001 PHE B 351 TRP 0.010 0.001 TRP A 220 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7703) covalent geometry : angle 1.18552 (10490) SS BOND : bond 0.00319 ( 1) SS BOND : angle 2.47916 ( 2) hydrogen bonds : bond 0.04404 ( 393) hydrogen bonds : angle 4.09066 ( 1128) link_BETA1-4 : bond 0.00488 ( 4) link_BETA1-4 : angle 2.08852 ( 12) link_NAG-ASN : bond 0.00345 ( 4) link_NAG-ASN : angle 4.44354 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.302 Fit side-chains REVERT: A 184 TRP cc_start: 0.8444 (m100) cc_final: 0.7879 (m-10) REVERT: A 269 GLN cc_start: 0.8894 (tp40) cc_final: 0.8686 (tt0) REVERT: A 356 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7934 (p0) REVERT: A 398 ASP cc_start: 0.7628 (p0) cc_final: 0.7280 (OUTLIER) REVERT: B 137 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9024 (tt) REVERT: B 218 GLN cc_start: 0.7894 (tp40) cc_final: 0.7473 (tm-30) REVERT: B 239 ASP cc_start: 0.7567 (t0) cc_final: 0.7262 (p0) REVERT: B 266 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: B 314 ASP cc_start: 0.8246 (m-30) cc_final: 0.7903 (m-30) REVERT: B 365 MET cc_start: 0.9295 (mtt) cc_final: 0.9013 (ttm) REVERT: B 392 ASP cc_start: 0.7884 (t0) cc_final: 0.7682 (t0) REVERT: B 421 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7230 (ptm-80) REVERT: B 451 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7652 (m-10) outliers start: 26 outliers final: 11 residues processed: 92 average time/residue: 0.3869 time to fit residues: 38.7471 Evaluate side-chains 75 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 5 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 47 GLN B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.077041 restraints weight = 13532.707| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.12 r_work: 0.2799 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7712 Z= 0.130 Angle : 1.191 33.189 10516 Z= 0.454 Chirality : 0.107 1.813 1233 Planarity : 0.004 0.050 1282 Dihedral : 22.458 178.233 1367 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.20 % Favored : 92.70 % Rotamer: Outliers : 3.04 % Allowed : 15.97 % 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 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: 0.12 (0.28), residues: 931 helix: 1.58 (0.24), residues: 503 sheet: -0.62 (0.62), residues: 67 loop : -2.06 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.013 0.001 TYR A 629 PHE 0.013 0.001 PHE B 351 TRP 0.007 0.001 TRP B 134 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7703) covalent geometry : angle 1.18106 (10490) SS BOND : bond 0.00991 ( 1) SS BOND : angle 3.07872 ( 2) hydrogen bonds : bond 0.04605 ( 393) hydrogen bonds : angle 4.08324 ( 1128) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 2.09033 ( 12) link_NAG-ASN : bond 0.00292 ( 4) link_NAG-ASN : angle 4.28233 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.279 Fit side-chains REVERT: A 184 TRP cc_start: 0.8470 (m100) cc_final: 0.7887 (m-10) REVERT: A 269 GLN cc_start: 0.8904 (tp40) cc_final: 0.8685 (tt0) REVERT: A 336 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: A 398 ASP cc_start: 0.7755 (p0) cc_final: 0.7334 (OUTLIER) REVERT: B 137 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8994 (tt) REVERT: B 218 GLN cc_start: 0.7732 (tp40) cc_final: 0.7342 (tm-30) REVERT: B 239 ASP cc_start: 0.7501 (t0) cc_final: 0.7250 (p0) REVERT: B 266 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: B 314 ASP cc_start: 0.8250 (m-30) cc_final: 0.7908 (m-30) REVERT: B 365 MET cc_start: 0.9272 (mtt) cc_final: 0.8981 (ttm) REVERT: B 392 ASP cc_start: 0.7970 (t0) cc_final: 0.7705 (t0) REVERT: B 421 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7340 (ptm-80) REVERT: B 451 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7559 (m-10) outliers start: 24 outliers final: 13 residues processed: 84 average time/residue: 0.4095 time to fit residues: 37.3395 Evaluate side-chains 74 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.077477 restraints weight = 13639.015| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.13 r_work: 0.2797 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7712 Z= 0.122 Angle : 1.181 32.844 10516 Z= 0.449 Chirality : 0.108 1.808 1233 Planarity : 0.004 0.049 1282 Dihedral : 22.387 178.561 1367 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.87 % Favored : 93.02 % Rotamer: Outliers : 3.30 % Allowed : 15.59 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.29), residues: 931 helix: 1.76 (0.24), residues: 501 sheet: -0.62 (0.61), residues: 67 loop : -1.94 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.013 0.001 TYR A 629 PHE 0.013 0.001 PHE B 351 TRP 0.010 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7703) covalent geometry : angle 1.17130 (10490) SS BOND : bond 0.00113 ( 1) SS BOND : angle 2.77232 ( 2) hydrogen bonds : bond 0.04450 ( 393) hydrogen bonds : angle 4.01084 ( 1128) link_BETA1-4 : bond 0.00504 ( 4) link_BETA1-4 : angle 2.03444 ( 12) link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 4.12763 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.303 Fit side-chains REVERT: A 184 TRP cc_start: 0.8446 (m100) cc_final: 0.7872 (m-10) REVERT: A 336 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: A 398 ASP cc_start: 0.7724 (p0) cc_final: 0.7313 (OUTLIER) REVERT: B 137 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9002 (tt) REVERT: B 218 GLN cc_start: 0.7721 (tp40) cc_final: 0.7380 (tm-30) REVERT: B 266 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: B 314 ASP cc_start: 0.8253 (m-30) cc_final: 0.7948 (m-30) REVERT: B 365 MET cc_start: 0.9274 (mtt) cc_final: 0.8983 (ttm) REVERT: B 421 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7429 (ptm-80) REVERT: B 451 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7641 (m-10) outliers start: 26 outliers final: 13 residues processed: 83 average time/residue: 0.4062 time to fit residues: 36.8519 Evaluate side-chains 71 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077307 restraints weight = 13657.394| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.14 r_work: 0.2797 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7712 Z= 0.131 Angle : 1.187 32.666 10516 Z= 0.454 Chirality : 0.108 1.811 1233 Planarity : 0.004 0.050 1282 Dihedral : 22.376 179.959 1367 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.20 % Favored : 92.70 % Rotamer: Outliers : 3.30 % Allowed : 15.84 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.29), residues: 931 helix: 1.85 (0.24), residues: 501 sheet: -0.61 (0.61), residues: 67 loop : -1.86 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.012 0.001 TYR A 629 PHE 0.015 0.001 PHE B 474 TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7703) covalent geometry : angle 1.17731 (10490) SS BOND : bond 0.00024 ( 1) SS BOND : angle 3.26011 ( 2) hydrogen bonds : bond 0.04525 ( 393) hydrogen bonds : angle 4.01984 ( 1128) link_BETA1-4 : bond 0.00453 ( 4) link_BETA1-4 : angle 2.01845 ( 12) link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 4.02525 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.258 Fit side-chains REVERT: A 170 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8472 (tm) REVERT: A 184 TRP cc_start: 0.8468 (m100) cc_final: 0.7891 (m-10) REVERT: A 336 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: A 398 ASP cc_start: 0.7695 (p0) cc_final: 0.7303 (OUTLIER) REVERT: B 218 GLN cc_start: 0.7719 (tp40) cc_final: 0.7369 (tm-30) REVERT: B 266 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: B 314 ASP cc_start: 0.8226 (m-30) cc_final: 0.7900 (m-30) REVERT: B 365 MET cc_start: 0.9272 (mtt) cc_final: 0.8975 (ttm) REVERT: B 421 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7508 (ptm-80) REVERT: B 451 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7610 (m-10) outliers start: 26 outliers final: 15 residues processed: 79 average time/residue: 0.4301 time to fit residues: 36.7520 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.076444 restraints weight = 13722.926| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.14 r_work: 0.2775 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7712 Z= 0.142 Angle : 1.190 32.528 10516 Z= 0.457 Chirality : 0.108 1.812 1233 Planarity : 0.004 0.050 1282 Dihedral : 22.374 179.393 1367 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.92 % Allowed : 16.22 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.29), residues: 931 helix: 1.92 (0.24), residues: 496 sheet: -0.63 (0.61), residues: 67 loop : -1.76 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.015 0.001 TYR A 629 PHE 0.014 0.001 PHE A 360 TRP 0.011 0.001 TRP B 477 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7703) covalent geometry : angle 1.18174 (10490) SS BOND : bond 0.00163 ( 1) SS BOND : angle 3.10265 ( 2) hydrogen bonds : bond 0.04761 ( 393) hydrogen bonds : angle 4.04222 ( 1128) link_BETA1-4 : bond 0.00542 ( 4) link_BETA1-4 : angle 1.99861 ( 12) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 3.91945 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.292 Fit side-chains REVERT: A 184 TRP cc_start: 0.8481 (m100) cc_final: 0.7903 (m-10) REVERT: A 336 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: A 398 ASP cc_start: 0.7699 (p0) cc_final: 0.7308 (OUTLIER) REVERT: B 218 GLN cc_start: 0.7715 (tp40) cc_final: 0.7378 (tm-30) REVERT: B 266 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: B 314 ASP cc_start: 0.8229 (m-30) cc_final: 0.7950 (m-30) REVERT: B 365 MET cc_start: 0.9263 (mtt) cc_final: 0.8952 (ttm) REVERT: B 421 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7581 (ptm-80) REVERT: B 451 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7614 (m-10) REVERT: B 507 THR cc_start: 0.4451 (OUTLIER) cc_final: 0.4166 (p) outliers start: 23 outliers final: 15 residues processed: 83 average time/residue: 0.4438 time to fit residues: 39.7352 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.077007 restraints weight = 13637.244| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.15 r_work: 0.2787 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7712 Z= 0.132 Angle : 1.187 32.399 10516 Z= 0.456 Chirality : 0.109 1.815 1233 Planarity : 0.004 0.050 1282 Dihedral : 22.347 179.016 1367 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.79 % Allowed : 16.86 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.29), residues: 931 helix: 1.99 (0.24), residues: 496 sheet: -0.59 (0.61), residues: 67 loop : -1.71 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.013 0.001 TYR A 629 PHE 0.022 0.001 PHE B 330 TRP 0.021 0.001 TRP B 477 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7703) covalent geometry : angle 1.17852 (10490) SS BOND : bond 0.00145 ( 1) SS BOND : angle 2.71876 ( 2) hydrogen bonds : bond 0.04573 ( 393) hydrogen bonds : angle 4.03447 ( 1128) link_BETA1-4 : bond 0.00492 ( 4) link_BETA1-4 : angle 1.98781 ( 12) link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 3.84810 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.292 Fit side-chains REVERT: A 184 TRP cc_start: 0.8473 (m100) cc_final: 0.7896 (m-10) REVERT: A 336 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: A 398 ASP cc_start: 0.7588 (p0) cc_final: 0.7269 (OUTLIER) REVERT: B 218 GLN cc_start: 0.7697 (tp40) cc_final: 0.7364 (tm-30) REVERT: B 266 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: B 314 ASP cc_start: 0.8216 (m-30) cc_final: 0.7910 (m-30) REVERT: B 365 MET cc_start: 0.9262 (mtt) cc_final: 0.8950 (ttm) REVERT: B 421 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7535 (ptm-80) REVERT: B 451 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7687 (m-10) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.3984 time to fit residues: 34.6873 Evaluate side-chains 74 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.075968 restraints weight = 13719.007| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.15 r_work: 0.2778 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7712 Z= 0.154 Angle : 1.202 32.479 10516 Z= 0.467 Chirality : 0.109 1.812 1233 Planarity : 0.004 0.049 1282 Dihedral : 22.338 178.906 1367 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.15 % Allowed : 17.62 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.29), residues: 931 helix: 1.96 (0.24), residues: 496 sheet: -0.60 (0.61), residues: 67 loop : -1.69 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.013 0.001 TYR A 629 PHE 0.015 0.001 PHE B 351 TRP 0.034 0.001 TRP B 477 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7703) covalent geometry : angle 1.19455 (10490) SS BOND : bond 0.00143 ( 1) SS BOND : angle 2.83391 ( 2) hydrogen bonds : bond 0.04866 ( 393) hydrogen bonds : angle 4.09349 ( 1128) link_BETA1-4 : bond 0.00460 ( 4) link_BETA1-4 : angle 1.98680 ( 12) link_NAG-ASN : bond 0.00209 ( 4) link_NAG-ASN : angle 3.80330 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.290 Fit side-chains REVERT: A 184 TRP cc_start: 0.8486 (m100) cc_final: 0.7910 (m-10) REVERT: A 398 ASP cc_start: 0.7599 (p0) cc_final: 0.7279 (OUTLIER) REVERT: A 562 GLU cc_start: 0.8483 (mp0) cc_final: 0.8238 (mm-30) REVERT: B 218 GLN cc_start: 0.7688 (tp40) cc_final: 0.7360 (tm-30) REVERT: B 266 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: B 314 ASP cc_start: 0.8229 (m-30) cc_final: 0.7945 (m-30) REVERT: B 365 MET cc_start: 0.9264 (mtt) cc_final: 0.8951 (ttm) REVERT: B 393 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 421 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7791 (tmt-80) REVERT: B 451 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7659 (m-10) outliers start: 17 outliers final: 14 residues processed: 74 average time/residue: 0.4199 time to fit residues: 33.8169 Evaluate side-chains 75 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.0050 chunk 90 optimal weight: 1.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.078298 restraints weight = 13484.367| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.10 r_work: 0.2818 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7712 Z= 0.120 Angle : 1.185 32.198 10516 Z= 0.456 Chirality : 0.109 1.823 1233 Planarity : 0.004 0.049 1282 Dihedral : 22.261 178.373 1367 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.28 % Allowed : 18.25 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 931 helix: 2.08 (0.24), residues: 497 sheet: -0.26 (0.69), residues: 52 loop : -1.62 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.011 0.001 TYR A 629 PHE 0.012 0.001 PHE B 351 TRP 0.030 0.001 TRP B 477 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7703) covalent geometry : angle 1.17804 (10490) SS BOND : bond 0.00157 ( 1) SS BOND : angle 2.40516 ( 2) hydrogen bonds : bond 0.04227 ( 393) hydrogen bonds : angle 3.99408 ( 1128) link_BETA1-4 : bond 0.00490 ( 4) link_BETA1-4 : angle 1.95931 ( 12) link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 3.69026 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.97 seconds wall clock time: 37 minutes 37.44 seconds (2257.44 seconds total)