Starting phenix.real_space_refine on Sat Oct 11 02:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iov_35626/10_2025/8iov_35626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iov_35626/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8iov_35626/10_2025/8iov_35626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iov_35626/10_2025/8iov_35626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iov_35626/10_2025/8iov_35626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iov_35626/10_2025/8iov_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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 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: 1.91, per 1000 atoms: 0.29 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: 0.70 Conformation dependent library (CDL) restraints added in 375.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 1.02 Time building geometry restraints manager: 0.91 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: 6.970 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.580 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- 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 : 5.82 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 aren 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 covalent geometry : bond 0.00313 ( 6791) covalent geometry : angle 0.62121 ( 9232) SS BOND : bond 0.00135 ( 7) SS BOND : angle 1.83345 ( 14) hydrogen bonds : bond 0.12130 ( 308) hydrogen bonds : angle 5.04275 ( 873) link_ALPHA1-3 : bond 0.00264 ( 1) link_ALPHA1-3 : angle 1.59110 ( 3) 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_NAG-ASN : bond 0.00866 ( 7) link_NAG-ASN : angle 5.15973 ( 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 : 0.284 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0756 time to fit residues: 6.2082 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 : 0.278 ------------------------------------------------------------------------------- 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... 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 = 0.3506 r_free = 0.3506 target = 0.079011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057511 restraints weight = 20945.820| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.89 r_work: 0.2827 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0711 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= 0.126 Angle : 0.607 9.932 9291 Z= 0.292 Chirality : 0.046 0.380 1012 Planarity : 0.003 0.036 1173 Dihedral : 10.184 68.530 1165 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.30), residues: 787 helix: 1.98 (0.26), residues: 394 sheet: 2.17 (0.75), residues: 42 loop : -0.67 (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 covalent geometry : bond 0.00272 ( 6791) covalent geometry : angle 0.56761 ( 9232) SS BOND : bond 0.00167 ( 7) SS BOND : angle 1.60357 ( 14) hydrogen bonds : bond 0.04658 ( 308) hydrogen bonds : angle 4.51202 ( 873) link_ALPHA1-3 : bond 0.00852 ( 1) link_ALPHA1-3 : angle 2.31659 ( 3) link_ALPHA1-6 : bond 0.00384 ( 1) link_ALPHA1-6 : angle 1.90263 ( 3) link_BETA1-4 : bond 0.00432 ( 6) link_BETA1-4 : angle 2.20005 ( 18) link_NAG-ASN : bond 0.00616 ( 7) link_NAG-ASN : angle 3.75165 ( 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 : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.0841 time to fit residues: 5.6538 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 : 0.263 ------------------------------------------------------------------------------- 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: 5.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.078146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056459 restraints weight = 20784.933| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.90 r_work: 0.2850 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0995 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= 0.130 Angle : 0.584 9.886 9291 Z= 0.280 Chirality : 0.045 0.358 1012 Planarity : 0.003 0.033 1173 Dihedral : 7.653 55.983 1165 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.96 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 aren not related in a simple way. whole: 1.26 (0.30), residues: 787 helix: 1.92 (0.26), residues: 401 sheet: 1.89 (0.77), residues: 42 loop : -0.62 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 115 TYR 0.011 0.001 TYR A 385 PHE 0.011 0.001 PHE B 342 TRP 0.014 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6791) covalent geometry : angle 0.54476 ( 9232) SS BOND : bond 0.00138 ( 7) SS BOND : angle 1.67189 ( 14) hydrogen bonds : bond 0.04715 ( 308) hydrogen bonds : angle 4.42665 ( 873) link_ALPHA1-3 : bond 0.00891 ( 1) link_ALPHA1-3 : angle 2.24944 ( 3) link_ALPHA1-6 : bond 0.01129 ( 1) link_ALPHA1-6 : angle 2.53862 ( 3) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 2.14652 ( 18) link_NAG-ASN : bond 0.00521 ( 7) link_NAG-ASN : angle 3.60276 ( 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 : 0.272 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.0832 time to fit residues: 5.4437 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 : 0.200 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.079004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057374 restraints weight = 20855.676| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.94 r_work: 0.2869 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6813 Z= 0.105 Angle : 0.554 9.988 9291 Z= 0.265 Chirality : 0.044 0.352 1012 Planarity : 0.003 0.035 1173 Dihedral : 6.239 48.891 1165 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.72 % Allowed : 6.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.30), residues: 787 helix: 1.99 (0.26), residues: 397 sheet: 1.84 (0.76), residues: 42 loop : -0.60 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.011 0.001 TYR A 50 PHE 0.010 0.001 PHE B 342 TRP 0.014 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6791) covalent geometry : angle 0.51675 ( 9232) SS BOND : bond 0.00115 ( 7) SS BOND : angle 1.53890 ( 14) hydrogen bonds : bond 0.04298 ( 308) hydrogen bonds : angle 4.31291 ( 873) link_ALPHA1-3 : bond 0.01135 ( 1) link_ALPHA1-3 : angle 2.17232 ( 3) link_ALPHA1-6 : bond 0.00652 ( 1) link_ALPHA1-6 : angle 1.68685 ( 3) link_BETA1-4 : bond 0.00398 ( 6) link_BETA1-4 : angle 1.95537 ( 18) link_NAG-ASN : bond 0.00542 ( 7) link_NAG-ASN : angle 3.55010 ( 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 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8690 (mp0) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.0815 time to fit residues: 5.6887 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 : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.078233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056533 restraints weight = 21183.071| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.99 r_work: 0.2797 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1306 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= 0.123 Angle : 0.558 10.182 9291 Z= 0.268 Chirality : 0.043 0.342 1012 Planarity : 0.003 0.034 1173 Dihedral : 5.628 40.231 1165 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 6.63 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.30), residues: 787 helix: 1.92 (0.26), residues: 404 sheet: 1.84 (0.78), residues: 42 loop : -0.52 (0.34), residues: 341 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 0.014 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6791) covalent geometry : angle 0.52159 ( 9232) SS BOND : bond 0.00123 ( 7) SS BOND : angle 1.63906 ( 14) hydrogen bonds : bond 0.04506 ( 308) hydrogen bonds : angle 4.31270 ( 873) link_ALPHA1-3 : bond 0.00905 ( 1) link_ALPHA1-3 : angle 1.86735 ( 3) link_ALPHA1-6 : bond 0.00673 ( 1) link_ALPHA1-6 : angle 1.64894 ( 3) link_BETA1-4 : bond 0.00372 ( 6) link_BETA1-4 : angle 1.89020 ( 18) link_NAG-ASN : bond 0.00462 ( 7) link_NAG-ASN : angle 3.51927 ( 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 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8591 (mt-10) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.0824 time to fit residues: 5.5612 Evaluate side-chains 51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.078462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056823 restraints weight = 21017.641| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.94 r_work: 0.2855 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6813 Z= 0.112 Angle : 0.554 9.734 9291 Z= 0.265 Chirality : 0.043 0.345 1012 Planarity : 0.003 0.035 1173 Dihedral : 5.171 33.903 1165 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.86 % Allowed : 7.64 % Favored : 91.50 % 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 aren not related in a simple way. whole: 1.36 (0.31), residues: 787 helix: 1.93 (0.26), residues: 404 sheet: 1.83 (0.78), residues: 42 loop : -0.47 (0.34), residues: 341 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 0.016 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6791) covalent geometry : angle 0.51824 ( 9232) SS BOND : bond 0.00106 ( 7) SS BOND : angle 1.59457 ( 14) hydrogen bonds : bond 0.04371 ( 308) hydrogen bonds : angle 4.27999 ( 873) link_ALPHA1-3 : bond 0.00911 ( 1) link_ALPHA1-3 : angle 1.78096 ( 3) link_ALPHA1-6 : bond 0.00708 ( 1) link_ALPHA1-6 : angle 1.60403 ( 3) link_BETA1-4 : bond 0.00389 ( 6) link_BETA1-4 : angle 1.81083 ( 18) link_NAG-ASN : bond 0.00486 ( 7) link_NAG-ASN : angle 3.49752 ( 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 : 0.277 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8619 (mt-10) REVERT: B 471 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8680 (mp0) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.0891 time to fit residues: 6.0880 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.078192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056525 restraints weight = 20824.280| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.96 r_work: 0.2844 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6813 Z= 0.122 Angle : 0.566 10.036 9291 Z= 0.272 Chirality : 0.043 0.345 1012 Planarity : 0.003 0.036 1173 Dihedral : 4.881 33.187 1165 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.86 % Allowed : 7.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.31), residues: 787 helix: 2.03 (0.26), residues: 402 sheet: 1.94 (0.80), residues: 41 loop : -0.55 (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 0.009 0.001 PHE B 342 TRP 0.018 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6791) covalent geometry : angle 0.53167 ( 9232) SS BOND : bond 0.00123 ( 7) SS BOND : angle 1.64134 ( 14) hydrogen bonds : bond 0.04445 ( 308) hydrogen bonds : angle 4.28027 ( 873) link_ALPHA1-3 : bond 0.00854 ( 1) link_ALPHA1-3 : angle 1.72995 ( 3) link_ALPHA1-6 : bond 0.00689 ( 1) link_ALPHA1-6 : angle 1.62300 ( 3) link_BETA1-4 : bond 0.00364 ( 6) link_BETA1-4 : angle 1.79342 ( 18) link_NAG-ASN : bond 0.00482 ( 7) link_NAG-ASN : angle 3.49843 ( 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 : 0.264 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9172 (mp0) cc_final: 0.8942 (mp0) REVERT: B 471 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8924 (mm-30) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.0818 time to fit residues: 5.6760 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 : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.056677 restraints weight = 20935.040| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.24 r_work: 0.2817 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1563 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= 0.100 Angle : 0.565 10.487 9291 Z= 0.269 Chirality : 0.042 0.337 1012 Planarity : 0.003 0.038 1173 Dihedral : 4.567 32.450 1165 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.58 % Allowed : 8.50 % 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 aren not related in a simple way. whole: 1.41 (0.31), residues: 787 helix: 1.97 (0.26), residues: 404 sheet: 1.84 (0.77), residues: 42 loop : -0.44 (0.35), residues: 341 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 0.007 0.001 PHE B 374 TRP 0.022 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 6791) covalent geometry : angle 0.53385 ( 9232) SS BOND : bond 0.00107 ( 7) SS BOND : angle 1.43094 ( 14) hydrogen bonds : bond 0.03999 ( 308) hydrogen bonds : angle 4.19886 ( 873) link_ALPHA1-3 : bond 0.00828 ( 1) link_ALPHA1-3 : angle 1.52351 ( 3) link_ALPHA1-6 : bond 0.00826 ( 1) link_ALPHA1-6 : angle 1.61863 ( 3) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 1.71535 ( 18) link_NAG-ASN : bond 0.00537 ( 7) link_NAG-ASN : angle 3.39693 ( 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 52 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8780 (mm) REVERT: A 474 MET cc_start: 0.8650 (mmp) cc_final: 0.8418 (mmt) REVERT: B 471 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8943 (mm-30) REVERT: B 478 LYS cc_start: 0.8474 (tptp) cc_final: 0.8218 (tptp) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.0810 time to fit residues: 5.7797 Evaluate side-chains 50 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.078024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055549 restraints weight = 21184.184| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.23 r_work: 0.2749 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1630 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= 0.120 Angle : 0.567 10.503 9291 Z= 0.271 Chirality : 0.042 0.334 1012 Planarity : 0.003 0.037 1173 Dihedral : 4.451 31.997 1165 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.72 % Allowed : 8.21 % Favored : 91.07 % 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 aren not related in a simple way. whole: 1.45 (0.31), residues: 787 helix: 1.98 (0.26), residues: 404 sheet: 2.06 (0.79), residues: 41 loop : -0.42 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.014 0.001 TYR A 50 PHE 0.008 0.001 PHE A 523 TRP 0.023 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6791) covalent geometry : angle 0.53526 ( 9232) SS BOND : bond 0.00140 ( 7) SS BOND : angle 1.57919 ( 14) hydrogen bonds : bond 0.04308 ( 308) hydrogen bonds : angle 4.24662 ( 873) link_ALPHA1-3 : bond 0.00721 ( 1) link_ALPHA1-3 : angle 1.60317 ( 3) link_ALPHA1-6 : bond 0.00760 ( 1) link_ALPHA1-6 : angle 1.64006 ( 3) link_BETA1-4 : bond 0.00352 ( 6) link_BETA1-4 : angle 1.75291 ( 18) link_NAG-ASN : bond 0.00423 ( 7) link_NAG-ASN : angle 3.33970 ( 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 53 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9213 (mp0) cc_final: 0.8920 (mp0) REVERT: B 471 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8945 (mm-30) REVERT: B 478 LYS cc_start: 0.8447 (tptp) cc_final: 0.8165 (tptp) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.0814 time to fit residues: 5.8450 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 : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.078399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.055780 restraints weight = 20956.375| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.24 r_work: 0.2801 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6813 Z= 0.106 Angle : 0.566 10.920 9291 Z= 0.272 Chirality : 0.042 0.336 1012 Planarity : 0.003 0.039 1173 Dihedral : 4.336 31.378 1165 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.72 % Allowed : 8.36 % 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 aren not related in a simple way. whole: 1.45 (0.31), residues: 787 helix: 1.98 (0.26), residues: 404 sheet: 2.05 (0.78), residues: 41 loop : -0.41 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.014 0.001 TYR A 50 PHE 0.008 0.001 PHE B 342 TRP 0.025 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6791) covalent geometry : angle 0.53552 ( 9232) SS BOND : bond 0.00106 ( 7) SS BOND : angle 1.49604 ( 14) hydrogen bonds : bond 0.04139 ( 308) hydrogen bonds : angle 4.24915 ( 873) link_ALPHA1-3 : bond 0.00737 ( 1) link_ALPHA1-3 : angle 1.51149 ( 3) link_ALPHA1-6 : bond 0.00822 ( 1) link_ALPHA1-6 : angle 1.63072 ( 3) link_BETA1-4 : bond 0.00385 ( 6) link_BETA1-4 : angle 1.69575 ( 18) link_NAG-ASN : bond 0.00483 ( 7) link_NAG-ASN : angle 3.30947 ( 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 53 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.9218 (mp0) cc_final: 0.8929 (mp0) REVERT: B 471 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8989 (mm-30) REVERT: B 478 LYS cc_start: 0.8518 (tptp) cc_final: 0.8222 (tptp) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.0837 time to fit residues: 5.8558 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.0040 chunk 73 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.078459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.056055 restraints weight = 20904.488| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.17 r_work: 0.2804 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6813 Z= 0.110 Angle : 0.570 10.841 9291 Z= 0.272 Chirality : 0.042 0.332 1012 Planarity : 0.003 0.039 1173 Dihedral : 4.256 31.064 1165 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.07 % 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 aren not related in a simple way. whole: 1.44 (0.31), residues: 787 helix: 1.98 (0.26), residues: 404 sheet: 2.02 (0.78), residues: 41 loop : -0.41 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.014 0.001 TYR A 50 PHE 0.008 0.001 PHE B 342 TRP 0.024 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6791) covalent geometry : angle 0.54092 ( 9232) SS BOND : bond 0.00115 ( 7) SS BOND : angle 1.51761 ( 14) hydrogen bonds : bond 0.04161 ( 308) hydrogen bonds : angle 4.23708 ( 873) link_ALPHA1-3 : bond 0.00674 ( 1) link_ALPHA1-3 : angle 1.50470 ( 3) link_ALPHA1-6 : bond 0.00795 ( 1) link_ALPHA1-6 : angle 1.61587 ( 3) link_BETA1-4 : bond 0.00356 ( 6) link_BETA1-4 : angle 1.68830 ( 18) link_NAG-ASN : bond 0.00456 ( 7) link_NAG-ASN : angle 3.26877 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.72 seconds wall clock time: 33 minutes 15.10 seconds (1995.10 seconds total)