Starting phenix.real_space_refine on Wed Mar 12 06:01:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ida_35361/03_2025/8ida_35361_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ida_35361/03_2025/8ida_35361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ida_35361/03_2025/8ida_35361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ida_35361/03_2025/8ida_35361.map" model { file = "/net/cci-nas-00/data/ceres_data/8ida_35361/03_2025/8ida_35361_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ida_35361/03_2025/8ida_35361_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 27 5.16 5 C 4816 2.51 5 N 1189 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7372 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3661 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 447} 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: "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: "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: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 6.24, per 1000 atoms: 0.85 Number of scatterers: 7372 At special positions: 0 Unit cell: (97.83, 81.525, 129.353, 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 27 16.00 O 1340 8.00 N 1189 7.00 C 4816 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=2.03 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 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 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 5 sheets defined 60.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.704A pdb=" N GLY A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 4.101A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.689A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.624A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.575A pdb=" N GLN A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.196A pdb=" N VAL A 327 " --> pdb=" O GLN A 323 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.565A pdb=" N ASN A 353 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.765A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.547A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.790A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.765A 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 80 removed outlier: 3.536A pdb=" N VAL B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Proline residue: B 72 - end of helix 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: 4.004A pdb=" N ALA B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 167 through 189 removed outlier: 4.042A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 221 removed outlier: 3.522A pdb=" N LYS B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 5.336A pdb=" N LEU B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 removed outlier: 3.708A pdb=" N THR B 264 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 298 Proline residue: B 275 - end of helix removed outlier: 3.664A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 4.042A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.503A 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 392 through 400 removed outlier: 4.250A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 422 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.708A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.757A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 removed outlier: 3.633A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.599A pdb=" N LEU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.001A 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: 6.857A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU A 225 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS A 432 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL A 466 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.327A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 621 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA5, first strand: chain 'B' and resid 365 through 366 393 hydrogen bonds defined for protein. 1143 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: 1.80 Time building geometry restraints manager: 2.53 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: 2250 1.34 - 1.46: 1279 1.46 - 1.58: 3984 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 7553 Sorted by residual: bond pdb=" CA TYR B 601 " pdb=" C TYR B 601 " ideal model delta sigma weight residual 1.525 1.489 0.036 2.10e-02 2.27e+03 2.87e+00 bond pdb=" CA TYR B 601 " pdb=" CB TYR B 601 " ideal model delta sigma weight residual 1.530 1.497 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" N TYR B 601 " pdb=" CA TYR B 601 " ideal model delta sigma weight residual 1.458 1.427 0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 1.409 1.440 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C3 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 7548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 10072 1.86 - 3.72: 169 3.72 - 5.58: 36 5.58 - 7.44: 5 7.44 - 9.31: 4 Bond angle restraints: 10286 Sorted by residual: angle pdb=" CA TYR B 601 " pdb=" CB TYR B 601 " pdb=" CG TYR B 601 " ideal model delta sigma weight residual 113.90 105.26 8.64 1.80e+00 3.09e-01 2.31e+01 angle pdb=" C ASP B 228 " pdb=" N PRO B 229 " pdb=" CA PRO B 229 " ideal model delta sigma weight residual 121.65 117.26 4.39 1.01e+00 9.80e-01 1.89e+01 angle pdb=" N GLY B 222 " pdb=" CA GLY B 222 " pdb=" C GLY B 222 " ideal model delta sigma weight residual 110.20 115.03 -4.83 1.32e+00 5.74e-01 1.34e+01 angle pdb=" N ARG B 421 " pdb=" CA ARG B 421 " pdb=" C ARG B 421 " ideal model delta sigma weight residual 112.23 116.66 -4.43 1.26e+00 6.30e-01 1.23e+01 angle pdb=" CA PRO A 602 " pdb=" N PRO A 602 " pdb=" CD PRO A 602 " ideal model delta sigma weight residual 112.00 107.43 4.57 1.40e+00 5.10e-01 1.07e+01 ... (remaining 10281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 4197 25.68 - 51.37: 240 51.37 - 77.05: 40 77.05 - 102.74: 25 102.74 - 128.42: 26 Dihedral angle restraints: 4528 sinusoidal: 1848 harmonic: 2680 Sorted by residual: dihedral pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " pdb=" C5 NAG D 2 " ideal model delta sinusoidal sigma weight residual -62.96 65.46 -128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sinusoidal sigma weight residual 175.11 58.60 116.51 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" O3 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sinusoidal sigma weight residual 295.45 178.97 116.48 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 4525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 1211 0.263 - 0.525: 2 0.525 - 0.788: 1 0.788 - 1.050: 0 1.050 - 1.313: 1 Chirality restraints: 1215 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.02e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.31e+01 ... (remaining 1212 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.358 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG E 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.344 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.515 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.336 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG F 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.095 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1230 2.76 - 3.30: 7173 3.30 - 3.83: 12087 3.83 - 4.37: 13466 4.37 - 4.90: 23897 Nonbonded interactions: 57853 Sorted by model distance: nonbonded pdb=" OG SER B 81 " pdb=" O ASN B 230 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 469 " pdb=" O PRO A 488 " model vdw 2.243 3.040 nonbonded pdb=" NH2 ARG A 604 " pdb=" O LYS A 616 " model vdw 2.250 3.120 nonbonded pdb=" O VAL B 224 " pdb=" ND2 ASN B 226 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.302 3.040 ... (remaining 57848 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.360 Find NCS groups from input model: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 0.062 7553 Z= 0.204 Angle : 0.617 9.305 10286 Z= 0.308 Chirality : 0.060 1.313 1215 Planarity : 0.021 0.306 1273 Dihedral : 20.753 128.423 2803 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.38 % Allowed : 0.25 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 930 helix: 1.94 (0.23), residues: 491 sheet: 0.17 (0.65), residues: 64 loop : -1.14 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 338 HIS 0.001 0.000 HIS B 420 PHE 0.016 0.001 PHE B 233 TYR 0.007 0.001 TYR B 259 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.803 Fit side-chains REVERT: A 319 TRP cc_start: 0.6455 (m100) cc_final: 0.5888 (m100) REVERT: B 78 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7936 (tp30) REVERT: B 158 LYS cc_start: 0.8849 (tppt) cc_final: 0.8635 (tptt) outliers start: 3 outliers final: 0 residues processed: 89 average time/residue: 0.1645 time to fit residues: 21.0381 Evaluate side-chains 66 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.0070 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.128289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097252 restraints weight = 11444.767| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.72 r_work: 0.3011 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7553 Z= 0.185 Angle : 0.622 9.358 10286 Z= 0.288 Chirality : 0.044 0.369 1215 Planarity : 0.004 0.034 1273 Dihedral : 19.752 104.283 1159 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.39 % Allowed : 7.10 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 930 helix: 2.23 (0.23), residues: 501 sheet: 0.14 (0.63), residues: 64 loop : -1.06 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.011 0.001 PHE B 200 TYR 0.007 0.001 TYR B 259 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.827 Fit side-chains REVERT: A 249 LEU cc_start: 0.7748 (tt) cc_final: 0.7478 (tt) REVERT: A 319 TRP cc_start: 0.6776 (m100) cc_final: 0.6167 (m100) REVERT: B 78 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8362 (tp30) REVERT: B 233 PHE cc_start: 0.7423 (t80) cc_final: 0.6855 (t80) REVERT: B 432 ASN cc_start: 0.7421 (m-40) cc_final: 0.6844 (t0) outliers start: 11 outliers final: 10 residues processed: 80 average time/residue: 0.1528 time to fit residues: 18.4732 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 63 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090351 restraints weight = 11659.919| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.84 r_work: 0.2920 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7553 Z= 0.238 Angle : 0.621 7.362 10286 Z= 0.289 Chirality : 0.044 0.313 1215 Planarity : 0.004 0.034 1273 Dihedral : 15.706 104.919 1159 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.28 % Allowed : 8.75 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 930 helix: 2.30 (0.23), residues: 501 sheet: 0.14 (0.63), residues: 64 loop : -1.12 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.003 0.001 HIS B 319 PHE 0.015 0.002 PHE B 200 TYR 0.012 0.001 TYR B 259 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.777 Fit side-chains REVERT: B 78 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8232 (tp30) REVERT: B 432 ASN cc_start: 0.7395 (m-40) cc_final: 0.6840 (t0) outliers start: 18 outliers final: 14 residues processed: 86 average time/residue: 0.1584 time to fit residues: 19.6616 Evaluate side-chains 77 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092451 restraints weight = 11524.241| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.86 r_work: 0.2952 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.171 Angle : 0.596 10.141 10286 Z= 0.273 Chirality : 0.042 0.258 1215 Planarity : 0.003 0.031 1273 Dihedral : 13.420 104.098 1159 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.41 % Allowed : 10.77 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.28), residues: 930 helix: 2.46 (0.24), residues: 498 sheet: 0.22 (0.64), residues: 66 loop : -1.11 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.001 0.000 HIS B 367 PHE 0.011 0.001 PHE A 542 TYR 0.006 0.001 TYR B 155 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 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: 19 poor density : 68 time to evaluate : 0.889 Fit side-chains REVERT: B 78 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8177 (tp30) REVERT: B 432 ASN cc_start: 0.7408 (m-40) cc_final: 0.6848 (t0) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.1459 time to fit residues: 18.0823 Evaluate side-chains 78 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.123264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092446 restraints weight = 11349.436| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.73 r_work: 0.2928 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.217 Angle : 0.611 10.247 10286 Z= 0.280 Chirality : 0.043 0.262 1215 Planarity : 0.003 0.031 1273 Dihedral : 11.928 106.306 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.41 % Allowed : 11.79 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.28), residues: 930 helix: 2.43 (0.23), residues: 498 sheet: 0.20 (0.64), residues: 66 loop : -1.11 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.013 0.001 PHE B 200 TYR 0.008 0.001 TYR B 146 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.870 Fit side-chains REVERT: B 78 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8470 (tp30) REVERT: B 432 ASN cc_start: 0.7440 (m-40) cc_final: 0.6826 (t0) outliers start: 19 outliers final: 17 residues processed: 83 average time/residue: 0.1647 time to fit residues: 19.9224 Evaluate side-chains 82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.123048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092187 restraints weight = 11377.120| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.71 r_work: 0.2929 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.220 Angle : 0.613 8.911 10286 Z= 0.281 Chirality : 0.042 0.243 1215 Planarity : 0.003 0.031 1273 Dihedral : 11.066 106.431 1159 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.28 % Allowed : 12.80 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.28), residues: 930 helix: 2.35 (0.24), residues: 501 sheet: 0.17 (0.64), residues: 66 loop : -1.11 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 319 PHE 0.016 0.001 PHE B 216 TYR 0.008 0.001 TYR A 454 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.755 Fit side-chains REVERT: B 78 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8451 (tp30) REVERT: B 432 ASN cc_start: 0.7449 (m-40) cc_final: 0.6835 (t0) outliers start: 18 outliers final: 17 residues processed: 78 average time/residue: 0.1674 time to fit residues: 19.3779 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.122990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092020 restraints weight = 11265.304| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.69 r_work: 0.2926 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.219 Angle : 0.619 11.747 10286 Z= 0.283 Chirality : 0.043 0.295 1215 Planarity : 0.003 0.031 1273 Dihedral : 10.351 106.582 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.28 % Allowed : 13.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 930 helix: 2.30 (0.24), residues: 501 sheet: 0.18 (0.64), residues: 66 loop : -1.09 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS A 539 PHE 0.013 0.001 PHE B 200 TYR 0.008 0.001 TYR A 454 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: B 78 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8430 (tp30) outliers start: 18 outliers final: 18 residues processed: 76 average time/residue: 0.1643 time to fit residues: 17.8808 Evaluate side-chains 80 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 65 optimal weight: 0.0470 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093962 restraints weight = 11405.637| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.81 r_work: 0.2978 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7553 Z= 0.154 Angle : 0.569 7.566 10286 Z= 0.262 Chirality : 0.041 0.259 1215 Planarity : 0.003 0.032 1273 Dihedral : 9.723 107.049 1159 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.03 % Allowed : 13.94 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 930 helix: 2.45 (0.24), residues: 498 sheet: 0.29 (0.65), residues: 66 loop : -0.99 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS A 539 PHE 0.012 0.001 PHE B 216 TYR 0.007 0.001 TYR A 423 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 1.009 Fit side-chains REVERT: A 580 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7329 (pp30) REVERT: B 78 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8282 (tp30) outliers start: 16 outliers final: 15 residues processed: 79 average time/residue: 0.1524 time to fit residues: 17.8023 Evaluate side-chains 77 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 451 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.122866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090811 restraints weight = 11547.010| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.81 r_work: 0.2932 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7553 Z= 0.205 Angle : 0.582 7.897 10286 Z= 0.272 Chirality : 0.042 0.242 1215 Planarity : 0.003 0.031 1273 Dihedral : 9.180 106.174 1159 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.41 % Allowed : 13.94 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 930 helix: 2.43 (0.24), residues: 498 sheet: 0.23 (0.64), residues: 66 loop : -0.99 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 220 HIS 0.001 0.001 HIS A 539 PHE 0.014 0.001 PHE B 200 TYR 0.009 0.001 TYR B 146 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 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: 19 poor density : 66 time to evaluate : 0.872 Fit side-chains REVERT: A 580 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7334 (pp30) REVERT: B 78 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8332 (tp30) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.1590 time to fit residues: 18.8090 Evaluate side-chains 74 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 85 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.124393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.093190 restraints weight = 11458.870| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.76 r_work: 0.2959 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7553 Z= 0.168 Angle : 0.573 7.615 10286 Z= 0.266 Chirality : 0.041 0.255 1215 Planarity : 0.003 0.032 1273 Dihedral : 8.772 106.422 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.03 % Allowed : 14.58 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 930 helix: 2.45 (0.24), residues: 498 sheet: 0.22 (0.64), residues: 66 loop : -0.94 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 319 HIS 0.002 0.001 HIS A 539 PHE 0.021 0.001 PHE B 216 TYR 0.006 0.001 TYR B 155 ARG 0.003 0.000 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 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: 16 poor density : 63 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 78 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8286 (tp30) outliers start: 16 outliers final: 15 residues processed: 75 average time/residue: 0.1474 time to fit residues: 16.6835 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 : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.123339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.092249 restraints weight = 11403.833| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.74 r_work: 0.2947 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.003 0.032 7553 Z= 0.189 Angle : 0.579 7.718 10286 Z= 0.272 Chirality : 0.041 0.255 1215 Planarity : 0.003 0.031 1273 Dihedral : 8.395 105.879 1159 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.03 % Allowed : 14.96 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 930 helix: 2.45 (0.24), residues: 498 sheet: 0.21 (0.64), residues: 66 loop : -0.93 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 319 HIS 0.002 0.001 HIS A 266 PHE 0.019 0.001 PHE B 216 TYR 0.008 0.001 TYR B 146 ARG 0.004 0.000 ARG A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.75 seconds wall clock time: 60 minutes 27.53 seconds (3627.53 seconds total)