Starting phenix.real_space_refine on Tue May 13 19:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iov_35626/05_2025/8iov_35626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iov_35626/05_2025/8iov_35626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iov_35626/05_2025/8iov_35626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iov_35626/05_2025/8iov_35626.map" model { file = "/net/cci-nas-00/data/ceres_data/8iov_35626/05_2025/8iov_35626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iov_35626/05_2025/8iov_35626.cif" } resolution = 3.29 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic. 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 37 5.16 5 C 4220 2.51 5 N 1075 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6607 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.30, per 1000 atoms: 0.80 Number of scatterers: 6607 At special positions: 0 Unit cell: (98.49, 72.36, 120.6, 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 37 16.00 O 1275 8.00 N 1075 7.00 C 4220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 432 " " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 975.7 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 55.1% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.529A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.983A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.781A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.996A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.878A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.762A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.693A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.040A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.675A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.286A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.507A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.536A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.890A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.554A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.707A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.056A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.028A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.781A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.668A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 873 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: 1.67 Time building geometry restraints manager: 2.31 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: 2080 1.34 - 1.46: 1702 1.46 - 1.58: 2951 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6791 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 9044 1.95 - 3.90: 150 3.90 - 5.85: 30 5.85 - 7.80: 6 7.80 - 9.76: 2 Bond angle restraints: 9232 Sorted by residual: angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" C ASN A 432 " pdb=" CA ASN A 432 " pdb=" CB ASN A 432 " ideal model delta sigma weight residual 110.84 106.14 4.70 1.66e+00 3.63e-01 8.01e+00 angle pdb=" CB MET A 190 " pdb=" CG MET A 190 " pdb=" SD MET A 190 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N GLU A 75 " pdb=" CA GLU A 75 " pdb=" CB GLU A 75 " ideal model delta sigma weight residual 110.16 114.01 -3.85 1.48e+00 4.57e-01 6.77e+00 angle pdb=" C ASP A 431 " pdb=" N ASN A 432 " pdb=" CA ASN A 432 " ideal model delta sigma weight residual 121.19 124.95 -3.76 1.59e+00 3.96e-01 5.59e+00 ... (remaining 9227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3981 21.98 - 43.96: 180 43.96 - 65.94: 14 65.94 - 87.92: 17 87.92 - 109.90: 8 Dihedral angle restraints: 4200 sinusoidal: 1876 harmonic: 2324 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -2.91 -83.09 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N GLU A 433 " pdb=" CA GLU A 433 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1006 0.230 - 0.459: 4 0.459 - 0.689: 1 0.689 - 0.919: 0 0.919 - 1.148: 1 Chirality restraints: 1012 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.25 -1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 1009 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " -0.033 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" CG ASN A 103 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 432 " 0.017 2.00e-02 2.50e+03 1.67e-02 3.50e+00 pdb=" CG ASN A 432 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 432 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 432 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 610 " 0.011 2.00e-02 2.50e+03 1.09e-02 2.95e+00 pdb=" CG TRP A 610 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 610 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 610 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 610 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 610 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 610 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 610 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 610 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 610 " -0.000 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1075 2.76 - 3.29: 6290 3.29 - 3.83: 10695 3.83 - 4.36: 12048 4.36 - 4.90: 21060 Nonbonded interactions: 51168 Sorted by model distance: nonbonded pdb=" OG SER A 607 " pdb=" OD1 ASP A 609 " model vdw 2.222 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.242 3.040 nonbonded pdb=" O GLY A 268 " pdb=" ND2 ASN A 277 " model vdw 2.293 3.120 nonbonded pdb=" O ALA B 344 " pdb=" OG1 THR B 345 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 489 " pdb=" OH TYR A 613 " model vdw 2.309 3.040 ... (remaining 51163 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' } 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: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.060 Process input model: 19.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 0.038 6813 Z= 0.160 Angle : 0.677 12.215 9291 Z= 0.311 Chirality : 0.060 1.148 1012 Planarity : 0.003 0.041 1173 Dihedral : 13.944 109.902 2687 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.31 (0.31), residues: 787 helix: 1.92 (0.26), residues: 397 sheet: 2.72 (0.76), residues: 42 loop : -0.63 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.007 0.001 PHE A 32 TYR 0.014 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00866 ( 7) link_NAG-ASN : angle 5.15973 ( 21) link_ALPHA1-6 : bond 0.00387 ( 1) link_ALPHA1-6 : angle 1.51806 ( 3) link_BETA1-4 : bond 0.00458 ( 6) link_BETA1-4 : angle 2.05393 ( 18) link_ALPHA1-3 : bond 0.00264 ( 1) link_ALPHA1-3 : angle 1.59110 ( 3) hydrogen bonds : bond 0.12130 ( 308) hydrogen bonds : angle 5.04275 ( 873) SS BOND : bond 0.00135 ( 7) SS BOND : angle 1.83345 ( 14) covalent geometry : bond 0.00313 ( 6791) covalent geometry : angle 0.62121 ( 9232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1740 time to fit residues: 14.0708 Evaluate side-chains 43 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 70 optimal weight: 0.0770 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058366 restraints weight = 20543.871| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.87 r_work: 0.2900 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6813 Z= 0.111 Angle : 0.597 10.012 9291 Z= 0.284 Chirality : 0.046 0.371 1012 Planarity : 0.003 0.036 1173 Dihedral : 9.766 65.093 1165 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.58 % Allowed : 4.61 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 787 helix: 2.01 (0.26), residues: 394 sheet: 2.12 (0.73), residues: 42 loop : -0.62 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 535 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.004 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 7) link_NAG-ASN : angle 3.71788 ( 21) link_ALPHA1-6 : bond 0.00634 ( 1) link_ALPHA1-6 : angle 1.71603 ( 3) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 2.25959 ( 18) link_ALPHA1-3 : bond 0.00846 ( 1) link_ALPHA1-3 : angle 2.29084 ( 3) hydrogen bonds : bond 0.04417 ( 308) hydrogen bonds : angle 4.44704 ( 873) SS BOND : bond 0.00151 ( 7) SS BOND : angle 1.47008 ( 14) covalent geometry : bond 0.00229 ( 6791) covalent geometry : angle 0.55768 ( 9232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1919 time to fit residues: 13.4752 Evaluate side-chains 45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.077743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056024 restraints weight = 20924.540| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.94 r_work: 0.2787 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6813 Z= 0.148 Angle : 0.592 10.013 9291 Z= 0.285 Chirality : 0.045 0.354 1012 Planarity : 0.003 0.033 1173 Dihedral : 7.511 55.715 1165 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.86 % Allowed : 6.34 % Favored : 92.80 % 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: 1.32 (0.30), residues: 787 helix: 2.01 (0.26), residues: 395 sheet: 1.90 (0.77), residues: 42 loop : -0.59 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 610 HIS 0.005 0.001 HIS A 401 PHE 0.012 0.001 PHE B 347 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 7) link_NAG-ASN : angle 3.60332 ( 21) link_ALPHA1-6 : bond 0.01023 ( 1) link_ALPHA1-6 : angle 2.40480 ( 3) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 2.16966 ( 18) link_ALPHA1-3 : bond 0.00827 ( 1) link_ALPHA1-3 : angle 2.23007 ( 3) hydrogen bonds : bond 0.04916 ( 308) hydrogen bonds : angle 4.43695 ( 873) SS BOND : bond 0.00144 ( 7) SS BOND : angle 1.73387 ( 14) covalent geometry : bond 0.00331 ( 6791) covalent geometry : angle 0.55356 ( 9232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1868 time to fit residues: 12.2328 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.076571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.054538 restraints weight = 21351.012| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.95 r_work: 0.2747 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6813 Z= 0.168 Angle : 0.608 9.976 9291 Z= 0.295 Chirality : 0.045 0.367 1012 Planarity : 0.003 0.033 1173 Dihedral : 6.362 51.215 1165 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.86 % Allowed : 7.06 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.31), residues: 787 helix: 1.86 (0.26), residues: 401 sheet: 1.88 (0.83), residues: 41 loop : -0.64 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 610 HIS 0.005 0.001 HIS A 401 PHE 0.014 0.001 PHE B 347 TYR 0.012 0.001 TYR A 50 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 7) link_NAG-ASN : angle 3.66294 ( 21) link_ALPHA1-6 : bond 0.00460 ( 1) link_ALPHA1-6 : angle 1.61401 ( 3) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 2.04660 ( 18) link_ALPHA1-3 : bond 0.00952 ( 1) link_ALPHA1-3 : angle 2.26911 ( 3) hydrogen bonds : bond 0.05177 ( 308) hydrogen bonds : angle 4.51591 ( 873) SS BOND : bond 0.00159 ( 7) SS BOND : angle 1.91724 ( 14) covalent geometry : bond 0.00381 ( 6791) covalent geometry : angle 0.56985 ( 9232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8661 (mp0) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1879 time to fit residues: 12.5398 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.077627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055707 restraints weight = 20933.226| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.95 r_work: 0.2777 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6813 Z= 0.117 Angle : 0.569 9.843 9291 Z= 0.275 Chirality : 0.044 0.357 1012 Planarity : 0.003 0.035 1173 Dihedral : 5.772 41.749 1165 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 7.49 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.31), residues: 787 helix: 1.92 (0.26), residues: 402 sheet: 1.74 (0.80), residues: 42 loop : -0.55 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.010 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 7) link_NAG-ASN : angle 3.61846 ( 21) link_ALPHA1-6 : bond 0.00637 ( 1) link_ALPHA1-6 : angle 1.66429 ( 3) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 1.87600 ( 18) link_ALPHA1-3 : bond 0.01025 ( 1) link_ALPHA1-3 : angle 1.82878 ( 3) hydrogen bonds : bond 0.04695 ( 308) hydrogen bonds : angle 4.38530 ( 873) SS BOND : bond 0.00109 ( 7) SS BOND : angle 1.74134 ( 14) covalent geometry : bond 0.00250 ( 6791) covalent geometry : angle 0.53139 ( 9232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8702 (mp0) outliers start: 5 outliers final: 1 residues processed: 45 average time/residue: 0.1914 time to fit residues: 12.0613 Evaluate side-chains 44 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.076258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.054331 restraints weight = 20744.170| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.96 r_work: 0.2740 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6813 Z= 0.170 Angle : 0.603 10.330 9291 Z= 0.293 Chirality : 0.044 0.358 1012 Planarity : 0.003 0.033 1173 Dihedral : 5.426 33.909 1165 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.72 % Allowed : 7.93 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.31), residues: 787 helix: 1.93 (0.26), residues: 402 sheet: 1.65 (0.82), residues: 43 loop : -0.59 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 610 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE B 347 TYR 0.012 0.001 TYR A 587 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 7) link_NAG-ASN : angle 3.67776 ( 21) link_ALPHA1-6 : bond 0.00594 ( 1) link_ALPHA1-6 : angle 1.65813 ( 3) link_BETA1-4 : bond 0.00331 ( 6) link_BETA1-4 : angle 1.91103 ( 18) link_ALPHA1-3 : bond 0.00865 ( 1) link_ALPHA1-3 : angle 1.95223 ( 3) hydrogen bonds : bond 0.05155 ( 308) hydrogen bonds : angle 4.46278 ( 873) SS BOND : bond 0.00158 ( 7) SS BOND : angle 1.94390 ( 14) covalent geometry : bond 0.00387 ( 6791) covalent geometry : angle 0.56613 ( 9232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8639 (mt-10) REVERT: B 471 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8672 (mp0) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.1727 time to fit residues: 11.4038 Evaluate side-chains 46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 48 optimal weight: 0.0070 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.077958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056239 restraints weight = 20576.870| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.91 r_work: 0.2791 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6813 Z= 0.110 Angle : 0.568 10.026 9291 Z= 0.274 Chirality : 0.043 0.353 1012 Planarity : 0.003 0.036 1173 Dihedral : 4.949 34.055 1165 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.29 % Allowed : 8.79 % Favored : 90.92 % 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: 1.36 (0.31), residues: 787 helix: 1.98 (0.26), residues: 402 sheet: 1.86 (0.80), residues: 41 loop : -0.54 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.008 0.001 PHE B 342 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 7) link_NAG-ASN : angle 3.60132 ( 21) link_ALPHA1-6 : bond 0.00778 ( 1) link_ALPHA1-6 : angle 1.65078 ( 3) link_BETA1-4 : bond 0.00416 ( 6) link_BETA1-4 : angle 1.75665 ( 18) link_ALPHA1-3 : bond 0.01005 ( 1) link_ALPHA1-3 : angle 1.70284 ( 3) hydrogen bonds : bond 0.04485 ( 308) hydrogen bonds : angle 4.32302 ( 873) SS BOND : bond 0.00109 ( 7) SS BOND : angle 1.71763 ( 14) covalent geometry : bond 0.00231 ( 6791) covalent geometry : angle 0.53152 ( 9232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8684 (mt-10) REVERT: B 471 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8968 (mm-30) outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.1739 time to fit residues: 11.2809 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.077167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.055177 restraints weight = 21070.770| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.03 r_work: 0.2761 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6813 Z= 0.135 Angle : 0.575 9.966 9291 Z= 0.278 Chirality : 0.043 0.351 1012 Planarity : 0.003 0.036 1173 Dihedral : 4.790 33.564 1165 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.43 % Allowed : 8.36 % Favored : 91.21 % 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: 1.36 (0.31), residues: 787 helix: 1.98 (0.26), residues: 402 sheet: 1.90 (0.82), residues: 41 loop : -0.53 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 7) link_NAG-ASN : angle 3.59281 ( 21) link_ALPHA1-6 : bond 0.00664 ( 1) link_ALPHA1-6 : angle 1.65610 ( 3) link_BETA1-4 : bond 0.00353 ( 6) link_BETA1-4 : angle 1.79814 ( 18) link_ALPHA1-3 : bond 0.00696 ( 1) link_ALPHA1-3 : angle 1.62547 ( 3) hydrogen bonds : bond 0.04741 ( 308) hydrogen bonds : angle 4.37114 ( 873) SS BOND : bond 0.00126 ( 7) SS BOND : angle 1.79733 ( 14) covalent geometry : bond 0.00304 ( 6791) covalent geometry : angle 0.53874 ( 9232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8962 (mm-30) REVERT: B 478 LYS cc_start: 0.8567 (tptp) cc_final: 0.8281 (tptp) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1757 time to fit residues: 11.3672 Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.077125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.054542 restraints weight = 20967.639| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.21 r_work: 0.2765 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6813 Z= 0.116 Angle : 0.565 10.248 9291 Z= 0.273 Chirality : 0.043 0.351 1012 Planarity : 0.003 0.037 1173 Dihedral : 4.611 33.409 1165 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.43 % Allowed : 8.65 % Favored : 90.92 % 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 (0.31), residues: 787 helix: 1.96 (0.26), residues: 402 sheet: 1.90 (0.81), residues: 41 loop : -0.52 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 PHE 0.009 0.001 PHE B 342 TYR 0.011 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 7) link_NAG-ASN : angle 3.53780 ( 21) link_ALPHA1-6 : bond 0.00745 ( 1) link_ALPHA1-6 : angle 1.64179 ( 3) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.73204 ( 18) link_ALPHA1-3 : bond 0.00815 ( 1) link_ALPHA1-3 : angle 1.57890 ( 3) hydrogen bonds : bond 0.04500 ( 308) hydrogen bonds : angle 4.33763 ( 873) SS BOND : bond 0.00107 ( 7) SS BOND : angle 1.72197 ( 14) covalent geometry : bond 0.00252 ( 6791) covalent geometry : angle 0.53040 ( 9232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8973 (mm-30) REVERT: B 478 LYS cc_start: 0.8514 (tptp) cc_final: 0.8206 (tptp) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1709 time to fit residues: 11.0830 Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.075769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053629 restraints weight = 21186.745| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.95 r_work: 0.2746 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6813 Z= 0.192 Angle : 0.621 10.417 9291 Z= 0.305 Chirality : 0.044 0.360 1012 Planarity : 0.003 0.034 1173 Dihedral : 4.776 33.116 1165 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.43 % Allowed : 8.65 % Favored : 90.92 % 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: 1.26 (0.31), residues: 787 helix: 1.91 (0.26), residues: 402 sheet: 1.62 (0.83), residues: 43 loop : -0.58 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 610 HIS 0.004 0.001 HIS A 34 PHE 0.011 0.001 PHE B 347 TYR 0.013 0.001 TYR A 587 ARG 0.002 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 7) link_NAG-ASN : angle 3.67021 ( 21) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 1.70548 ( 3) link_BETA1-4 : bond 0.00298 ( 6) link_BETA1-4 : angle 1.85559 ( 18) link_ALPHA1-3 : bond 0.00744 ( 1) link_ALPHA1-3 : angle 1.77817 ( 3) hydrogen bonds : bond 0.05399 ( 308) hydrogen bonds : angle 4.55489 ( 873) SS BOND : bond 0.00177 ( 7) SS BOND : angle 1.97637 ( 14) covalent geometry : bond 0.00444 ( 6791) covalent geometry : angle 0.58523 ( 9232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 498 CYS cc_start: 0.8873 (t) cc_final: 0.7887 (t) REVERT: B 471 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8964 (mm-30) REVERT: B 478 LYS cc_start: 0.8572 (tptp) cc_final: 0.8258 (tptp) outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.1777 time to fit residues: 11.1963 Evaluate side-chains 46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.076434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053899 restraints weight = 21083.055| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.16 r_work: 0.2748 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6813 Z= 0.131 Angle : 0.595 10.081 9291 Z= 0.289 Chirality : 0.044 0.362 1012 Planarity : 0.003 0.037 1173 Dihedral : 4.645 33.268 1165 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 9.08 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.31), residues: 787 helix: 1.90 (0.26), residues: 402 sheet: 1.64 (0.81), residues: 43 loop : -0.54 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 610 HIS 0.003 0.001 HIS A 34 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 7) link_NAG-ASN : angle 3.60844 ( 21) link_ALPHA1-6 : bond 0.00724 ( 1) link_ALPHA1-6 : angle 1.65202 ( 3) link_BETA1-4 : bond 0.00352 ( 6) link_BETA1-4 : angle 1.72221 ( 18) link_ALPHA1-3 : bond 0.00740 ( 1) link_ALPHA1-3 : angle 1.54358 ( 3) hydrogen bonds : bond 0.04890 ( 308) hydrogen bonds : angle 4.46372 ( 873) SS BOND : bond 0.00116 ( 7) SS BOND : angle 1.87406 ( 14) covalent geometry : bond 0.00291 ( 6791) covalent geometry : angle 0.56034 ( 9232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3339.87 seconds wall clock time: 59 minutes 6.84 seconds (3546.84 seconds total)