Starting phenix.real_space_refine on Thu Jul 2 23:25:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_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 { model { file = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iov_35626/07_2026/8iov_35626.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.18 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: 0.42 Conformation dependent library (CDL) restraints added in 250.1 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: 0.17 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: 0.66 Time building geometry restraints manager: 0.57 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 - 16.62: 3569 16.62 - 33.24: 284 33.24 - 49.86: 33 49.86 - 66.48: 2 66.48 - 83.09: 5 Dihedral angle restraints: 3893 sinusoidal: 1569 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 3890 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 11.465 81.498 2380 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (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 ARG 0.001 0.000 ARG A 169 TYR 0.014 0.001 TYR A 50 PHE 0.007 0.001 PHE A 32 TRP 0.030 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 6791) covalent geometry : angle 0.62121 / 0.30 ( 9232) SS BOND : bond 0.00135 / 0.07 ( 7) SS BOND : angle 1.83345 / 1.06 ( 14) hydrogen bonds : bond 0.12130 / 7.63 ( 308) hydrogen bonds : angle 5.04275 / 3.60 ( 873) link_ALPHA1-3 : bond 0.00264 / 0.14 ( 1) link_ALPHA1-3 : angle 1.59110 / 0.88 ( 3) link_ALPHA1-6 : bond 0.00387 / 0.20 ( 1) link_ALPHA1-6 : angle 1.51806 / 0.84 ( 3) link_BETA1-4 : bond 0.00458 / 0.23 ( 6) link_BETA1-4 : angle 2.05393 / 1.18 ( 18) link_NAG-ASN : bond 0.00866 / 0.45 ( 7) link_NAG-ASN : angle 5.15973 / 3.10 ( 21) *********************** 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 : 0.196 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0619 time to fit residues: 5.0252 Evaluate side-chains 42 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.057421 restraints weight = 20933.014| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.91 r_work: 0.2826 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6813 Z= 0.125 Angle : 0.589 9.726 9291 Z= 0.288 Chirality : 0.044 0.349 1012 Planarity : 0.003 0.035 1173 Dihedral : 4.096 19.049 858 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.58 % Allowed : 4.47 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.30), residues: 787 helix: 1.98 (0.26), residues: 394 sheet: 2.12 (0.75), residues: 42 loop : -0.66 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.012 0.001 TYR A 50 PHE 0.010 0.001 PHE B 342 TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6791) covalent geometry : angle 0.55490 / 0.28 ( 9232) SS BOND : bond 0.00160 / 0.10 ( 7) SS BOND : angle 1.60593 / 0.91 ( 14) hydrogen bonds : bond 0.04636 / 3.13 ( 308) hydrogen bonds : angle 4.50193 / 3.18 ( 873) link_ALPHA1-3 : bond 0.00944 / 0.50 ( 1) link_ALPHA1-3 : angle 1.64638 / 0.91 ( 3) link_ALPHA1-6 : bond 0.00330 / 0.17 ( 1) link_ALPHA1-6 : angle 1.61867 / 0.89 ( 3) link_BETA1-4 : bond 0.00335 / 0.18 ( 6) link_BETA1-4 : angle 1.66672 / 0.96 ( 18) link_NAG-ASN : bond 0.00576 / 0.29 ( 7) link_NAG-ASN : angle 3.61311 / 2.12 ( 21) *********************** 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 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.0603 time to fit residues: 4.1115 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 : 0.150 ------------------------------------------------------------------------------- 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 18 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.056780 restraints weight = 20767.878| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.90 r_work: 0.2808 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6813 Z= 0.126 Angle : 0.566 10.038 9291 Z= 0.274 Chirality : 0.043 0.338 1012 Planarity : 0.003 0.034 1173 Dihedral : 4.045 18.796 858 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 5.91 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.30), residues: 787 helix: 1.92 (0.26), residues: 401 sheet: 1.92 (0.75), residues: 42 loop : -0.62 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.010 0.001 TYR A 50 PHE 0.010 0.001 PHE B 342 TRP 0.013 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6791) covalent geometry : angle 0.53343 / 0.27 ( 9232) SS BOND : bond 0.00133 / 0.08 ( 7) SS BOND : angle 1.63812 / 0.92 ( 14) hydrogen bonds : bond 0.04640 / 3.15 ( 308) hydrogen bonds : angle 4.42365 / 3.13 ( 873) link_ALPHA1-3 : bond 0.00564 / 0.30 ( 1) link_ALPHA1-3 : angle 1.39418 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00395 / 0.21 ( 1) link_ALPHA1-6 : angle 1.55488 / 0.85 ( 3) link_BETA1-4 : bond 0.00404 / 0.20 ( 6) link_BETA1-4 : angle 1.53725 / 0.91 ( 18) link_NAG-ASN : bond 0.00536 / 0.27 ( 7) link_NAG-ASN : angle 3.47781 / 2.05 ( 21) *********************** 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 : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0654 time to fit residues: 4.3577 Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.078134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056476 restraints weight = 20954.635| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.95 r_work: 0.2798 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6813 Z= 0.123 Angle : 0.557 9.751 9291 Z= 0.270 Chirality : 0.043 0.336 1012 Planarity : 0.003 0.034 1173 Dihedral : 4.016 18.833 858 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.01 % Allowed : 6.34 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.30), residues: 787 helix: 1.95 (0.26), residues: 401 sheet: 1.84 (0.77), residues: 42 loop : -0.57 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.012 0.001 TYR A 50 PHE 0.010 0.001 PHE B 342 TRP 0.013 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6791) covalent geometry : angle 0.52520 / 0.26 ( 9232) SS BOND : bond 0.00121 / 0.07 ( 7) SS BOND : angle 1.63680 / 0.92 ( 14) hydrogen bonds : bond 0.04589 / 3.13 ( 308) hydrogen bonds : angle 4.38715 / 3.11 ( 873) link_ALPHA1-3 : bond 0.00478 / 0.25 ( 1) link_ALPHA1-3 : angle 1.44104 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00478 / 0.25 ( 1) link_ALPHA1-6 : angle 1.57617 / 0.87 ( 3) link_BETA1-4 : bond 0.00397 / 0.20 ( 6) link_BETA1-4 : angle 1.46499 / 0.87 ( 18) link_NAG-ASN : bond 0.00482 / 0.25 ( 7) link_NAG-ASN : angle 3.45471 / 2.03 ( 21) *********************** 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 54 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.177 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.0619 time to fit residues: 4.3755 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 : 0.235 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056266 restraints weight = 21176.579| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.97 r_work: 0.2789 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6813 Z= 0.123 Angle : 0.561 10.040 9291 Z= 0.271 Chirality : 0.042 0.335 1012 Planarity : 0.003 0.034 1173 Dihedral : 3.983 18.802 858 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.30), residues: 787 helix: 1.92 (0.26), residues: 402 sheet: 1.71 (0.77), residues: 42 loop : -0.56 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.012 0.001 TYR A 50 PHE 0.010 0.001 PHE B 342 TRP 0.015 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6791) covalent geometry : angle 0.52918 / 0.26 ( 9232) SS BOND : bond 0.00116 / 0.07 ( 7) SS BOND : angle 1.67998 / 0.94 ( 14) hydrogen bonds : bond 0.04592 / 3.12 ( 308) hydrogen bonds : angle 4.35071 / 3.08 ( 873) link_ALPHA1-3 : bond 0.00326 / 0.17 ( 1) link_ALPHA1-3 : angle 1.38207 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00266 / 0.14 ( 1) link_ALPHA1-6 : angle 1.44715 / 0.79 ( 3) link_BETA1-4 : bond 0.00389 / 0.20 ( 6) link_BETA1-4 : angle 1.43671 / 0.85 ( 18) link_NAG-ASN : bond 0.00468 / 0.24 ( 7) link_NAG-ASN : angle 3.44828 / 2.02 ( 21) *********************** 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 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9161 (mp0) cc_final: 0.8955 (mp0) REVERT: B 406 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8585 (mt-10) REVERT: B 471 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8647 (mp0) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0708 time to fit residues: 4.6043 Evaluate side-chains 49 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.055665 restraints weight = 21147.187| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.00 r_work: 0.2770 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6813 Z= 0.135 Angle : 0.561 9.615 9291 Z= 0.272 Chirality : 0.042 0.335 1012 Planarity : 0.003 0.034 1173 Dihedral : 3.995 18.880 858 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.86 % Allowed : 7.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.31), residues: 787 helix: 1.96 (0.26), residues: 402 sheet: 1.79 (0.80), residues: 41 loop : -0.57 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.012 0.001 TYR A 50 PHE 0.010 0.001 PHE B 342 TRP 0.016 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6791) covalent geometry : angle 0.52831 / 0.26 ( 9232) SS BOND : bond 0.00129 / 0.08 ( 7) SS BOND : angle 1.75763 / 0.97 ( 14) hydrogen bonds : bond 0.04724 / 3.22 ( 308) hydrogen bonds : angle 4.35833 / 3.08 ( 873) link_ALPHA1-3 : bond 0.00395 / 0.21 ( 1) link_ALPHA1-3 : angle 1.47453 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00294 / 0.15 ( 1) link_ALPHA1-6 : angle 1.46420 / 0.80 ( 3) link_BETA1-4 : bond 0.00366 / 0.18 ( 6) link_BETA1-4 : angle 1.43760 / 0.84 ( 18) link_NAG-ASN : bond 0.00448 / 0.23 ( 7) link_NAG-ASN : angle 3.47058 / 2.04 ( 21) *********************** 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 54 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8630 (mt-10) REVERT: B 471 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8676 (mp0) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.0714 time to fit residues: 4.8402 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 : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 474 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 55 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055868 restraints weight = 20776.440| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.94 r_work: 0.2779 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6813 Z= 0.127 Angle : 0.571 9.849 9291 Z= 0.277 Chirality : 0.043 0.338 1012 Planarity : 0.003 0.034 1173 Dihedral : 3.987 18.895 858 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 8.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.31), residues: 787 helix: 2.00 (0.26), residues: 402 sheet: 1.85 (0.80), residues: 41 loop : -0.54 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.012 0.001 TYR A 50 PHE 0.009 0.001 PHE B 342 TRP 0.019 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6791) covalent geometry : angle 0.53915 / 0.27 ( 9232) SS BOND : bond 0.00120 / 0.07 ( 7) SS BOND : angle 1.74544 / 0.97 ( 14) hydrogen bonds : bond 0.04640 / 3.17 ( 308) hydrogen bonds : angle 4.34580 / 3.07 ( 873) link_ALPHA1-3 : bond 0.00399 / 0.21 ( 1) link_ALPHA1-3 : angle 1.46141 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00285 / 0.15 ( 1) link_ALPHA1-6 : angle 1.45819 / 0.80 ( 3) link_BETA1-4 : bond 0.00361 / 0.18 ( 6) link_BETA1-4 : angle 1.41937 / 0.83 ( 18) link_NAG-ASN : bond 0.00462 / 0.24 ( 7) link_NAG-ASN : angle 3.45224 / 2.02 ( 21) *********************** 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 53 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9164 (mp0) cc_final: 0.8954 (mp0) REVERT: B 471 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8705 (mp0) REVERT: B 478 LYS cc_start: 0.8574 (tptp) cc_final: 0.8284 (tptp) outliers start: 6 outliers final: 2 residues processed: 48 average time/residue: 0.0595 time to fit residues: 4.0722 Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054860 restraints weight = 21025.435| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.98 r_work: 0.2757 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6813 Z= 0.153 Angle : 0.591 9.776 9291 Z= 0.287 Chirality : 0.043 0.341 1012 Planarity : 0.003 0.035 1173 Dihedral : 4.035 19.032 858 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.58 % Allowed : 8.65 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.31), residues: 787 helix: 1.98 (0.26), residues: 402 sheet: 1.63 (0.81), residues: 43 loop : -0.54 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.012 0.001 TYR A 50 PHE 0.010 0.001 PHE B 347 TRP 0.020 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6791) covalent geometry : angle 0.55987 / 0.28 ( 9232) SS BOND : bond 0.00143 / 0.09 ( 7) SS BOND : angle 1.83805 / 1.01 ( 14) hydrogen bonds : bond 0.04905 / 3.35 ( 308) hydrogen bonds : angle 4.39820 / 3.10 ( 873) link_ALPHA1-3 : bond 0.00340 / 0.18 ( 1) link_ALPHA1-3 : angle 1.50453 / 0.83 ( 3) link_ALPHA1-6 : bond 0.00265 / 0.14 ( 1) link_ALPHA1-6 : angle 1.47354 / 0.81 ( 3) link_BETA1-4 : bond 0.00342 / 0.17 ( 6) link_BETA1-4 : angle 1.45753 / 0.85 ( 18) link_NAG-ASN : bond 0.00465 / 0.24 ( 7) link_NAG-ASN : angle 3.50086 / 2.05 ( 21) *********************** 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 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9141 (mp0) cc_final: 0.8928 (mp0) REVERT: B 471 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8667 (mp0) outliers start: 4 outliers final: 4 residues processed: 46 average time/residue: 0.0654 time to fit residues: 4.2013 Evaluate side-chains 49 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054952 restraints weight = 21165.716| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.94 r_work: 0.2759 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1661 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= 0.145 Angle : 0.588 9.874 9291 Z= 0.287 Chirality : 0.043 0.344 1012 Planarity : 0.003 0.035 1173 Dihedral : 4.049 19.103 858 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.72 % Allowed : 8.79 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.31), residues: 787 helix: 1.94 (0.26), residues: 402 sheet: 1.57 (0.81), residues: 43 loop : -0.55 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.012 0.001 TYR A 50 PHE 0.009 0.001 PHE B 342 TRP 0.023 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6791) covalent geometry : angle 0.55666 / 0.28 ( 9232) SS BOND : bond 0.00120 / 0.08 ( 7) SS BOND : angle 1.83861 / 1.01 ( 14) hydrogen bonds : bond 0.04905 / 3.35 ( 308) hydrogen bonds : angle 4.41668 / 3.12 ( 873) link_ALPHA1-3 : bond 0.00350 / 0.18 ( 1) link_ALPHA1-3 : angle 1.49293 / 0.83 ( 3) link_ALPHA1-6 : bond 0.00255 / 0.13 ( 1) link_ALPHA1-6 : angle 1.46979 / 0.81 ( 3) link_BETA1-4 : bond 0.00343 / 0.17 ( 6) link_BETA1-4 : angle 1.44344 / 0.84 ( 18) link_NAG-ASN : bond 0.00454 / 0.23 ( 7) link_NAG-ASN : angle 3.49439 / 2.05 ( 21) *********************** 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 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8901 (mm-30) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.0645 time to fit residues: 4.4869 Evaluate side-chains 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 0.0030 chunk 33 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.077038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054513 restraints weight = 20955.724| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.15 r_work: 0.2767 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6813 Z= 0.122 Angle : 0.592 10.319 9291 Z= 0.285 Chirality : 0.042 0.344 1012 Planarity : 0.003 0.037 1173 Dihedral : 4.003 18.969 858 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.72 % Allowed : 8.65 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.31), residues: 787 helix: 1.93 (0.26), residues: 402 sheet: 1.79 (0.81), residues: 41 loop : -0.54 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.011 0.001 TYR A 50 PHE 0.008 0.001 PHE B 342 TRP 0.025 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6791) covalent geometry : angle 0.56226 / 0.28 ( 9232) SS BOND : bond 0.00117 / 0.07 ( 7) SS BOND : angle 1.76872 / 0.98 ( 14) hydrogen bonds : bond 0.04662 / 3.17 ( 308) hydrogen bonds : angle 4.39486 / 3.10 ( 873) link_ALPHA1-3 : bond 0.00386 / 0.20 ( 1) link_ALPHA1-3 : angle 1.45356 / 0.80 ( 3) link_ALPHA1-6 : bond 0.00235 / 0.12 ( 1) link_ALPHA1-6 : angle 1.42959 / 0.79 ( 3) link_BETA1-4 : bond 0.00329 / 0.17 ( 6) link_BETA1-4 : angle 1.38677 / 0.81 ( 18) link_NAG-ASN : bond 0.00487 / 0.25 ( 7) link_NAG-ASN : angle 3.44066 / 2.02 ( 21) ********************** 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 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9188 (mp0) cc_final: 0.8950 (mp0) REVERT: B 471 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8919 (mm-30) REVERT: B 478 LYS cc_start: 0.8462 (tptp) cc_final: 0.8178 (tptp) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 0.0630 time to fit residues: 4.3476 Evaluate side-chains 48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.649 > 50: distance: 83 - 107: 31.123 distance: 89 - 115: 22.902 distance: 101 - 107: 29.511 distance: 107 - 108: 39.992 distance: 108 - 109: 34.152 distance: 108 - 111: 25.808 distance: 109 - 110: 46.655 distance: 109 - 115: 36.018 distance: 111 - 112: 28.666 distance: 112 - 113: 7.754 distance: 112 - 114: 30.889 distance: 115 - 116: 7.455 distance: 116 - 117: 37.007 distance: 116 - 119: 21.937 distance: 117 - 118: 41.098 distance: 117 - 126: 9.210 distance: 119 - 120: 37.342 distance: 120 - 121: 22.296 distance: 121 - 122: 19.181 distance: 122 - 123: 8.666 distance: 123 - 124: 5.291 distance: 123 - 125: 13.174 distance: 126 - 127: 14.986 distance: 127 - 128: 24.019 distance: 127 - 130: 24.514 distance: 128 - 129: 31.265 distance: 128 - 134: 13.923 distance: 130 - 131: 41.027 distance: 131 - 132: 14.868 distance: 131 - 133: 52.908 distance: 134 - 135: 14.550 distance: 135 - 136: 29.100 distance: 136 - 137: 10.847 distance: 136 - 138: 30.597 distance: 138 - 139: 9.317 distance: 139 - 140: 40.785 distance: 139 - 142: 4.388 distance: 140 - 141: 36.432 distance: 140 - 147: 23.369 distance: 142 - 143: 32.722 distance: 143 - 144: 23.404 distance: 144 - 145: 37.430 distance: 145 - 146: 17.995 distance: 147 - 148: 23.666 distance: 148 - 149: 28.428 distance: 148 - 151: 13.720 distance: 149 - 150: 40.053 distance: 149 - 153: 28.601 distance: 151 - 152: 10.114 distance: 153 - 154: 26.938 distance: 154 - 157: 25.325 distance: 155 - 156: 31.472 distance: 155 - 162: 27.869 distance: 157 - 158: 20.984 distance: 158 - 159: 7.386 distance: 159 - 160: 39.976 distance: 159 - 161: 51.401 distance: 162 - 163: 23.064 distance: 162 - 168: 6.626 distance: 163 - 164: 30.903 distance: 163 - 166: 34.630 distance: 164 - 165: 12.576 distance: 164 - 169: 20.376 distance: 165 - 197: 33.710 distance: 167 - 168: 36.430 distance: 170 - 171: 34.077 distance: 170 - 173: 40.448 distance: 171 - 172: 13.602 distance: 171 - 183: 40.774 distance: 172 - 202: 22.617 distance: 173 - 174: 25.735 distance: 174 - 175: 11.265 distance: 174 - 176: 27.975 distance: 175 - 177: 39.332 distance: 176 - 178: 50.646 distance: 176 - 179: 33.447 distance: 177 - 178: 39.220 distance: 178 - 180: 38.917 distance: 179 - 181: 16.999 distance: 180 - 182: 9.647 distance: 181 - 182: 18.596 distance: 183 - 184: 14.237 distance: 184 - 185: 37.996 distance: 184 - 187: 23.730 distance: 185 - 186: 15.517 distance: 185 - 190: 34.041 distance: 186 - 209: 26.402 distance: 187 - 188: 39.448 distance: 187 - 189: 49.408