Starting phenix.real_space_refine on Thu Jul 2 16:15:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ty6_26167/07_2026/7ty6_26167.cif" } resolution = 2.98 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= -0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 5824 2.51 5 N 1320 2.21 5 O 1482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 8672 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4169 Chain: "B" Number of atoms: 4082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4169 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: "A" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 194 Unusual residues: {'4DS': 1, 'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 194 Unusual residues: {'4DS': 1, 'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Time building chain proxies: 2.50, per 1000 atoms: 0.29 Number of scatterers: 8672 At special positions: 0 Unit cell: (112.98, 95.764, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 1482 8.00 N 1320 7.00 C 5824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 452.0 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 73.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.734A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.586A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.559A pdb=" N ILE A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 594 Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.648A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 701 through 718 removed outlier: 3.650A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.665A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.825A pdb=" N ARG A 827 " --> pdb=" O PRO A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.686A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.734A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.585A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.548A pdb=" N ILE B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 594 Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.650A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 701 through 718 removed outlier: 3.648A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.663A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.825A pdb=" N ARG B 827 " --> pdb=" O PRO B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.688A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 741 removed outlier: 3.877A pdb=" N GLU A 755 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 741 removed outlier: 3.863A pdb=" N GLU B 755 " --> pdb=" O VAL B 740 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1524 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: 0.96 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1396 1.33 - 1.45: 2166 1.45 - 1.57: 5202 1.57 - 1.70: 8 1.70 - 1.82: 70 Bond restraints: 8842 Sorted by residual: bond pdb=" CAK 4DS B2204 " pdb=" CAL 4DS B2204 " ideal model delta sigma weight residual 1.336 1.541 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" CAK 4DS A2204 " pdb=" CAL 4DS A2204 " ideal model delta sigma weight residual 1.336 1.533 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" CAT 4DS B2204 " pdb=" NAS 4DS B2204 " ideal model delta sigma weight residual 1.170 1.322 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" CBA 4DS A2204 " pdb=" NAZ 4DS A2204 " ideal model delta sigma weight residual 1.170 1.318 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" CBA 4DS B2204 " pdb=" NAZ 4DS B2204 " ideal model delta sigma weight residual 1.170 1.318 -0.148 2.00e-02 2.50e+03 5.50e+01 ... (remaining 8837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.13: 12047 11.13 - 22.27: 1 22.27 - 33.40: 0 33.40 - 44.54: 0 44.54 - 55.67: 6 Bond angle restraints: 12054 Sorted by residual: angle pdb=" CAP 4DS A2204 " pdb=" NAS 4DS A2204 " pdb=" CAT 4DS A2204 " ideal model delta sigma weight residual 180.00 124.33 55.67 3.00e+00 1.11e-01 3.44e+02 angle pdb=" CAP 4DS B2204 " pdb=" NAS 4DS B2204 " pdb=" CAT 4DS B2204 " ideal model delta sigma weight residual 180.00 124.43 55.57 3.00e+00 1.11e-01 3.43e+02 angle pdb=" NAS 4DS A2204 " pdb=" CAT 4DS A2204 " pdb=" SAU 4DS A2204 " ideal model delta sigma weight residual 180.00 125.79 54.21 3.00e+00 1.11e-01 3.27e+02 angle pdb=" NAS 4DS B2204 " pdb=" CAT 4DS B2204 " pdb=" SAU 4DS B2204 " ideal model delta sigma weight residual 180.00 126.11 53.89 3.00e+00 1.11e-01 3.23e+02 angle pdb=" CAG 4DS A2204 " pdb=" NAZ 4DS A2204 " pdb=" CBA 4DS A2204 " ideal model delta sigma weight residual 177.62 125.11 52.51 3.00e+00 1.11e-01 3.06e+02 ... (remaining 12049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4656 17.34 - 34.68: 320 34.68 - 52.02: 89 52.02 - 69.36: 27 69.36 - 86.71: 14 Dihedral angle restraints: 5106 sinusoidal: 2122 harmonic: 2984 Sorted by residual: dihedral pdb=" C ASN B 554 " pdb=" N ASN B 554 " pdb=" CA ASN B 554 " pdb=" CB ASN B 554 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C ASN A 554 " pdb=" N ASN A 554 " pdb=" CA ASN A 554 " pdb=" CB ASN A 554 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" CA GLN B 374 " pdb=" C GLN B 374 " pdb=" N THR B 375 " pdb=" CA THR B 375 " ideal model delta harmonic sigma weight residual 180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 722 0.067 - 0.135: 573 0.135 - 0.202: 135 0.202 - 0.269: 5 0.269 - 0.337: 3 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.83e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.31e+01 chirality pdb=" CA ASN B 554 " pdb=" N ASN B 554 " pdb=" C ASN B 554 " pdb=" CB ASN B 554 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1435 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG C 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.327 2.00e-02 2.50e+03 2.78e-01 9.68e+02 pdb=" C7 NAG D 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAP 4DS A2204 " 0.111 2.00e-02 2.50e+03 2.22e-01 4.92e+02 pdb=" CAT 4DS A2204 " 0.285 2.00e-02 2.50e+03 pdb=" NAS 4DS A2204 " -0.309 2.00e-02 2.50e+03 pdb=" SAU 4DS A2204 " -0.087 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1992 2.87 - 3.38: 9513 3.38 - 3.89: 14846 3.89 - 4.39: 17699 4.39 - 4.90: 29025 Nonbonded interactions: 73075 Sorted by model distance: nonbonded pdb=" O LEU B 863 " pdb=" OG1 THR B 866 " model vdw 2.366 3.040 nonbonded pdb=" O LEU A 863 " pdb=" OG1 THR A 866 " model vdw 2.381 3.040 nonbonded pdb=" O THR A 686 " pdb=" OG SER A 690 " model vdw 2.396 3.040 nonbonded pdb=" O THR B 686 " pdb=" OG SER B 690 " model vdw 2.397 3.040 nonbonded pdb=" O THR A 727 " pdb=" OG SER A 731 " model vdw 2.448 3.040 ... (remaining 73070 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 369 through 650 or resid 652 through 2206)) selection = (chain 'B' and (resid 369 through 650 or resid 652 through 2206)) } 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.014 0.205 8848 Z= 1.036 Angle : 2.159 55.672 12066 Z= 1.418 Chirality : 0.086 0.337 1438 Planarity : 0.016 0.291 1414 Dihedral : 14.416 86.705 3182 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.89 % Allowed : 4.89 % Favored : 94.22 % Cbeta Deviations : 0.21 % 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: -2.86 (0.21), residues: 1026 helix: -1.62 (0.16), residues: 692 sheet: None (None), residues: 0 loop : -2.17 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 760 TYR 0.013 0.003 TYR B 824 PHE 0.018 0.003 PHE B 675 TRP 0.026 0.004 TRP A 492 HIS 0.005 0.002 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.01377 / 1.01 ( 8842) covalent geometry : angle 2.15611 / 1.42 (12054) hydrogen bonds : bond 0.23216 / 15.51 ( 522) hydrogen bonds : angle 8.08905 / 5.77 ( 1524) Misc. bond : bond 0.14713 / 7.35 ( 2) link_BETA1-4 : bond 0.00949 / 0.48 ( 2) link_BETA1-4 : angle 2.46546 / 1.28 ( 6) link_NAG-ASN : bond 0.00262 / 0.13 ( 2) link_NAG-ASN : angle 5.58940 / 2.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 880 ASN cc_start: 0.9403 (t0) cc_final: 0.9154 (t0) REVERT: B 473 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8841 (tp30) REVERT: B 880 ASN cc_start: 0.9396 (t0) cc_final: 0.9152 (t0) outliers start: 8 outliers final: 2 residues processed: 75 average time/residue: 0.5339 time to fit residues: 42.6152 Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ARG Chi-restraints excluded: chain B residue 603 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 ASN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.046063 restraints weight = 58181.001| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.36 r_work: 0.2477 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8848 Z= 0.159 Angle : 0.722 13.061 12066 Z= 0.336 Chirality : 0.041 0.175 1438 Planarity : 0.005 0.048 1414 Dihedral : 10.226 85.325 1280 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.67 % Allowed : 9.11 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1026 helix: 0.97 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 589 TYR 0.010 0.001 TYR B 555 PHE 0.017 0.001 PHE B 411 TRP 0.017 0.002 TRP B 492 HIS 0.004 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 8842) covalent geometry : angle 0.72010 / 0.34 (12054) hydrogen bonds : bond 0.05487 / 3.71 ( 522) hydrogen bonds : angle 4.61009 / 3.31 ( 1524) Misc. bond : bond 0.00153 / 0.07 ( 2) link_BETA1-4 : bond 0.00253 / 0.13 ( 2) link_BETA1-4 : angle 1.80060 / 1.02 ( 6) link_NAG-ASN : bond 0.00353 / 0.18 ( 2) link_NAG-ASN : angle 1.92703 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 429 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8735 (mp0) REVERT: A 663 MET cc_start: 0.9339 (mmm) cc_final: 0.8694 (tpp) REVERT: A 721 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9128 (mmm) REVERT: B 473 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8552 (tm-30) REVERT: B 559 MET cc_start: 0.8645 (mmm) cc_final: 0.8325 (mmm) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.5619 time to fit residues: 29.4848 Evaluate side-chains 46 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 ASN A 554 ASN B 554 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.045559 restraints weight = 52119.117| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.13 r_work: 0.2487 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8848 Z= 0.151 Angle : 0.641 11.235 12066 Z= 0.294 Chirality : 0.040 0.196 1438 Planarity : 0.005 0.052 1414 Dihedral : 9.495 81.789 1272 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.33 % Allowed : 8.56 % Favored : 90.11 % 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: 1.03 (0.26), residues: 1026 helix: 1.55 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.27 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 602 TYR 0.010 0.001 TYR A 519 PHE 0.013 0.001 PHE B 411 TRP 0.013 0.001 TRP B 492 HIS 0.004 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8842) covalent geometry : angle 0.63930 / 0.29 (12054) hydrogen bonds : bond 0.04575 / 3.08 ( 522) hydrogen bonds : angle 4.28348 / 3.08 ( 1524) Misc. bond : bond 0.00192 / 0.09 ( 2) link_BETA1-4 : bond 0.00265 / 0.13 ( 2) link_BETA1-4 : angle 1.67120 / 1.06 ( 6) link_NAG-ASN : bond 0.00211 / 0.11 ( 2) link_NAG-ASN : angle 1.10681 / 0.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8713 (mmm) cc_final: 0.8456 (mmm) REVERT: A 664 MET cc_start: 0.9171 (ttm) cc_final: 0.8932 (ttp) REVERT: A 721 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8618 (mpp) REVERT: B 473 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 559 MET cc_start: 0.8723 (mmm) cc_final: 0.8323 (mmm) REVERT: B 603 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8727 (mpp-170) outliers start: 12 outliers final: 4 residues processed: 54 average time/residue: 0.4779 time to fit residues: 27.6513 Evaluate side-chains 48 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 ASN B 554 ASN B 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.044359 restraints weight = 77502.703| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 4.83 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8848 Z= 0.170 Angle : 0.638 11.565 12066 Z= 0.291 Chirality : 0.040 0.167 1438 Planarity : 0.005 0.052 1414 Dihedral : 9.099 78.583 1272 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.33 % Allowed : 8.78 % Favored : 89.89 % 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: 1.32 (0.26), residues: 1026 helix: 1.72 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 490 TYR 0.009 0.001 TYR B 519 PHE 0.013 0.001 PHE B 471 TRP 0.017 0.002 TRP B 492 HIS 0.002 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 8842) covalent geometry : angle 0.63661 / 0.29 (12054) hydrogen bonds : bond 0.04394 / 2.97 ( 522) hydrogen bonds : angle 4.16232 / 2.99 ( 1524) Misc. bond : bond 0.00112 / 0.06 ( 2) link_BETA1-4 : bond 0.00215 / 0.11 ( 2) link_BETA1-4 : angle 1.41462 / 0.95 ( 6) link_NAG-ASN : bond 0.00256 / 0.13 ( 2) link_NAG-ASN : angle 1.05210 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 MET cc_start: 0.8734 (mmm) cc_final: 0.8451 (mmm) REVERT: A 586 MET cc_start: 0.9313 (mmm) cc_final: 0.9062 (mmt) REVERT: A 721 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8833 (mmm) REVERT: B 473 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 603 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8407 (mpp-170) REVERT: B 721 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8369 (mpp) outliers start: 12 outliers final: 4 residues processed: 53 average time/residue: 0.4463 time to fit residues: 25.5658 Evaluate side-chains 49 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain B residue 603 ARG Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 ASN B 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.045021 restraints weight = 74936.808| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 4.81 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8848 Z= 0.129 Angle : 0.614 10.568 12066 Z= 0.279 Chirality : 0.039 0.164 1438 Planarity : 0.005 0.051 1414 Dihedral : 8.824 77.702 1272 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.89 % Allowed : 8.22 % Favored : 89.89 % 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: 1.50 (0.27), residues: 1026 helix: 1.83 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.89 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.010 0.001 TYR B 519 PHE 0.014 0.001 PHE B 411 TRP 0.014 0.001 TRP A 492 HIS 0.002 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8842) covalent geometry : angle 0.61307 / 0.28 (12054) hydrogen bonds : bond 0.04110 / 2.77 ( 522) hydrogen bonds : angle 4.07396 / 2.93 ( 1524) Misc. bond : bond 0.00122 / 0.06 ( 2) link_BETA1-4 : bond 0.00397 / 0.20 ( 2) link_BETA1-4 : angle 1.31799 / 0.91 ( 6) link_NAG-ASN : bond 0.00124 / 0.06 ( 2) link_NAG-ASN : angle 0.82019 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9124 (m110) cc_final: 0.8860 (m110) REVERT: A 559 MET cc_start: 0.8755 (mmm) cc_final: 0.8409 (mmm) REVERT: A 586 MET cc_start: 0.9330 (mmm) cc_final: 0.9081 (mmt) REVERT: A 663 MET cc_start: 0.9204 (tpt) cc_final: 0.8852 (tpt) REVERT: A 721 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8827 (mmm) REVERT: B 473 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8214 (tm-30) REVERT: B 721 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8153 (mpp) outliers start: 17 outliers final: 5 residues processed: 53 average time/residue: 0.5120 time to fit residues: 29.1698 Evaluate side-chains 49 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 76 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.045790 restraints weight = 56418.381| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 4.29 r_work: 0.2494 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8848 Z= 0.118 Angle : 0.595 10.161 12066 Z= 0.271 Chirality : 0.039 0.162 1438 Planarity : 0.005 0.050 1414 Dihedral : 8.506 76.632 1272 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.22 % Allowed : 8.44 % Favored : 90.33 % 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: 1.64 (0.27), residues: 1026 helix: 1.93 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.81 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 603 TYR 0.010 0.001 TYR A 519 PHE 0.013 0.001 PHE A 411 TRP 0.014 0.001 TRP B 492 HIS 0.002 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8842) covalent geometry : angle 0.59398 / 0.27 (12054) hydrogen bonds : bond 0.03952 / 2.67 ( 522) hydrogen bonds : angle 4.01055 / 2.88 ( 1524) Misc. bond : bond 0.00119 / 0.06 ( 2) link_BETA1-4 : bond 0.00269 / 0.14 ( 2) link_BETA1-4 : angle 1.20689 / 0.83 ( 6) link_NAG-ASN : bond 0.00087 / 0.04 ( 2) link_NAG-ASN : angle 0.76662 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9117 (m110) cc_final: 0.8844 (m110) REVERT: A 559 MET cc_start: 0.8713 (mmm) cc_final: 0.8311 (mmm) REVERT: A 586 MET cc_start: 0.9516 (mmm) cc_final: 0.9304 (mmt) REVERT: A 663 MET cc_start: 0.9297 (tpt) cc_final: 0.8820 (tpt) REVERT: A 721 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8490 (mpp) REVERT: B 603 ARG cc_start: 0.8677 (mpp80) cc_final: 0.8472 (mpp80) REVERT: B 721 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8740 (mpt) outliers start: 11 outliers final: 4 residues processed: 50 average time/residue: 0.4825 time to fit residues: 25.8774 Evaluate side-chains 48 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 819 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.044938 restraints weight = 79544.213| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 4.92 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8848 Z= 0.135 Angle : 0.619 11.874 12066 Z= 0.278 Chirality : 0.039 0.158 1438 Planarity : 0.005 0.050 1414 Dihedral : 8.389 75.981 1272 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.00 % Allowed : 9.22 % Favored : 89.78 % 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: 1.72 (0.27), residues: 1026 helix: 1.98 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 518 TYR 0.010 0.001 TYR B 519 PHE 0.013 0.001 PHE A 471 TRP 0.013 0.001 TRP A 492 HIS 0.002 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8842) covalent geometry : angle 0.61848 / 0.28 (12054) hydrogen bonds : bond 0.04006 / 2.71 ( 522) hydrogen bonds : angle 4.00614 / 2.88 ( 1524) Misc. bond : bond 0.00103 / 0.05 ( 2) link_BETA1-4 : bond 0.00318 / 0.16 ( 2) link_BETA1-4 : angle 1.22744 / 0.89 ( 6) link_NAG-ASN : bond 0.00134 / 0.07 ( 2) link_NAG-ASN : angle 0.82970 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9080 (m110) cc_final: 0.8814 (m110) REVERT: A 559 MET cc_start: 0.8710 (mmm) cc_final: 0.8278 (mmm) REVERT: A 586 MET cc_start: 0.9354 (mmm) cc_final: 0.9093 (mmt) REVERT: A 663 MET cc_start: 0.9203 (tpt) cc_final: 0.8856 (tpt) REVERT: A 721 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8831 (mmm) REVERT: B 603 ARG cc_start: 0.8379 (mpp80) cc_final: 0.8117 (ptp-110) REVERT: B 721 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8185 (mpp) outliers start: 9 outliers final: 4 residues processed: 45 average time/residue: 0.4967 time to fit residues: 23.9320 Evaluate side-chains 48 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.054683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.043971 restraints weight = 59679.448| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 4.37 r_work: 0.2442 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8848 Z= 0.187 Angle : 0.649 11.528 12066 Z= 0.294 Chirality : 0.040 0.154 1438 Planarity : 0.005 0.049 1414 Dihedral : 8.494 75.335 1272 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.89 % Allowed : 9.44 % Favored : 89.67 % 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: 1.65 (0.27), residues: 1026 helix: 1.89 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.73 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 602 TYR 0.009 0.001 TYR B 519 PHE 0.013 0.001 PHE A 471 TRP 0.016 0.001 TRP B 492 HIS 0.001 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8842) covalent geometry : angle 0.64862 / 0.29 (12054) hydrogen bonds : bond 0.04282 / 2.90 ( 522) hydrogen bonds : angle 4.07741 / 2.94 ( 1524) Misc. bond : bond 0.00080 / 0.04 ( 2) link_BETA1-4 : bond 0.00072 / 0.03 ( 2) link_BETA1-4 : angle 1.19456 / 0.89 ( 6) link_NAG-ASN : bond 0.00279 / 0.14 ( 2) link_NAG-ASN : angle 1.03036 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9150 (m110) cc_final: 0.8883 (m110) REVERT: A 559 MET cc_start: 0.8639 (mmm) cc_final: 0.8184 (mmm) REVERT: A 586 MET cc_start: 0.9498 (mmm) cc_final: 0.9286 (mmt) REVERT: A 663 MET cc_start: 0.9338 (tpt) cc_final: 0.8942 (tpt) REVERT: B 559 MET cc_start: 0.8777 (mmt) cc_final: 0.8378 (mmm) REVERT: B 603 ARG cc_start: 0.8637 (mpp80) cc_final: 0.8354 (ptp-110) REVERT: B 721 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8422 (mpp) outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 0.5008 time to fit residues: 23.6099 Evaluate side-chains 45 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.2942 r_free = 0.2942 target = 0.055689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.044802 restraints weight = 73688.359| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 4.79 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8848 Z= 0.125 Angle : 0.617 11.777 12066 Z= 0.279 Chirality : 0.039 0.152 1438 Planarity : 0.005 0.049 1414 Dihedral : 8.291 75.786 1272 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.56 % Allowed : 9.78 % Favored : 89.67 % 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: 1.74 (0.27), residues: 1026 helix: 1.95 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 603 TYR 0.010 0.001 TYR B 519 PHE 0.013 0.001 PHE A 471 TRP 0.012 0.001 TRP A 492 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 8842) covalent geometry : angle 0.61671 / 0.28 (12054) hydrogen bonds : bond 0.04025 / 2.73 ( 522) hydrogen bonds : angle 4.02210 / 2.90 ( 1524) Misc. bond : bond 0.00104 / 0.05 ( 2) link_BETA1-4 : bond 0.00249 / 0.12 ( 2) link_BETA1-4 : angle 1.04279 / 0.76 ( 6) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 0.77629 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9090 (m110) cc_final: 0.8827 (m110) REVERT: A 559 MET cc_start: 0.8621 (mmm) cc_final: 0.8202 (mmm) REVERT: A 586 MET cc_start: 0.9342 (mmm) cc_final: 0.9088 (mmt) REVERT: A 663 MET cc_start: 0.9235 (tpt) cc_final: 0.8846 (tpt) REVERT: B 559 MET cc_start: 0.8738 (mmt) cc_final: 0.8358 (mmm) REVERT: B 603 ARG cc_start: 0.8340 (mpp80) cc_final: 0.8080 (ptp-110) REVERT: B 721 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8192 (mpp) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.4754 time to fit residues: 24.5219 Evaluate side-chains 49 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.2961 r_free = 0.2961 target = 0.056504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.045569 restraints weight = 72676.560| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 4.80 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8848 Z= 0.115 Angle : 0.607 11.756 12066 Z= 0.275 Chirality : 0.038 0.154 1438 Planarity : 0.005 0.049 1414 Dihedral : 8.067 75.683 1272 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.56 % Allowed : 10.11 % Favored : 89.33 % 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: 1.82 (0.27), residues: 1026 helix: 2.04 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.67 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 603 TYR 0.010 0.001 TYR B 519 PHE 0.012 0.001 PHE B 471 TRP 0.015 0.001 TRP A 492 HIS 0.002 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 8842) covalent geometry : angle 0.60705 / 0.27 (12054) hydrogen bonds : bond 0.03844 / 2.60 ( 522) hydrogen bonds : angle 3.97184 / 2.86 ( 1524) Misc. bond : bond 0.00111 / 0.06 ( 2) link_BETA1-4 : bond 0.00204 / 0.10 ( 2) link_BETA1-4 : angle 1.07395 / 0.78 ( 6) link_NAG-ASN : bond 0.00026 / 0.01 ( 2) link_NAG-ASN : angle 0.82033 / 0.43 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 ASN cc_start: 0.9064 (m110) cc_final: 0.8838 (m110) REVERT: A 559 MET cc_start: 0.8604 (mmm) cc_final: 0.8197 (mmm) REVERT: A 586 MET cc_start: 0.9361 (mmm) cc_final: 0.9108 (mmt) REVERT: A 663 MET cc_start: 0.9216 (tpt) cc_final: 0.8853 (tpt) REVERT: B 559 MET cc_start: 0.8750 (mmt) cc_final: 0.8354 (mmm) REVERT: B 603 ARG cc_start: 0.8334 (mpp80) cc_final: 0.8079 (ptp-110) REVERT: B 721 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8206 (mpp) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.4205 time to fit residues: 21.8859 Evaluate side-chains 50 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 833 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 819 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.045921 restraints weight = 69186.138| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 4.72 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8848 Z= 0.110 Angle : 0.589 10.725 12066 Z= 0.269 Chirality : 0.038 0.148 1438 Planarity : 0.005 0.049 1414 Dihedral : 7.927 75.406 1272 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.56 % Allowed : 10.11 % Favored : 89.33 % 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: 1.88 (0.27), residues: 1026 helix: 2.05 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 603 TYR 0.011 0.001 TYR A 486 PHE 0.012 0.001 PHE A 471 TRP 0.012 0.001 TRP A 492 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8842) covalent geometry : angle 0.58865 / 0.27 (12054) hydrogen bonds : bond 0.03785 / 2.57 ( 522) hydrogen bonds : angle 3.94524 / 2.85 ( 1524) Misc. bond : bond 0.00120 / 0.06 ( 2) link_BETA1-4 : bond 0.00240 / 0.12 ( 2) link_BETA1-4 : angle 1.01905 / 0.76 ( 6) link_NAG-ASN : bond 0.00017 / 0.01 ( 2) link_NAG-ASN : angle 0.82793 / 0.43 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.17 seconds wall clock time: 30 minutes 39.55 seconds (1839.55 seconds total)