Starting phenix.real_space_refine on Thu Jul 2 14:11:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v19_26954/07_2026/7v19_26954.map" } resolution = 3.3 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= 0.109 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 6 5.49 5 S 38 5.16 5 C 5968 2.51 5 N 1408 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 8936 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8936 At special positions: 0 Unit cell: (146.495, 91.3, 80.925, 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 38 16.00 P 6 15.00 O 1516 8.00 N 1408 7.00 C 5968 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=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 195.5 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 74.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 88 through 114 Processing helix chain 'D' and resid 88 through 114 Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 402 through 431 removed outlier: 3.614A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 465 through 483 Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.596A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 516 removed outlier: 3.599A pdb=" N LEU C 512 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 547 removed outlier: 3.533A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.765A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'C' and resid 661 through 667 removed outlier: 3.788A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 703 through 719 removed outlier: 3.533A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 760 through 772 Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 784 through 799 removed outlier: 3.722A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 811 Processing helix chain 'C' and resid 812 through 814 No H-bonds generated for 'chain 'C' and resid 812 through 814' Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 829 through 852 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 865 through 872 removed outlier: 3.547A pdb=" N LEU C 869 " --> pdb=" O LEU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 877 Processing helix chain 'C' and resid 879 through 887 Processing helix chain 'E' and resid 379 through 390 Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 402 through 431 removed outlier: 3.575A pdb=" N LEU E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 436 through 455 Processing helix chain 'E' and resid 465 through 482 Processing helix chain 'E' and resid 485 through 507 removed outlier: 3.789A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.508A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 547 Processing helix chain 'E' and resid 569 through 594 removed outlier: 3.728A pdb=" N ASN E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 608 Processing helix chain 'E' and resid 608 through 623 Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.848A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 690 Processing helix chain 'E' and resid 691 through 695 Processing helix chain 'E' and resid 701 through 719 removed outlier: 3.772A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE E 719 " --> pdb=" O VAL E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 738 Processing helix chain 'E' and resid 760 through 772 Processing helix chain 'E' and resid 776 through 781 Processing helix chain 'E' and resid 784 through 799 removed outlier: 3.869A pdb=" N LEU E 788 " --> pdb=" O PRO E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 811 Processing helix chain 'E' and resid 812 through 814 No H-bonds generated for 'chain 'E' and resid 812 through 814' Processing helix chain 'E' and resid 815 through 819 Processing helix chain 'E' and resid 822 through 827 Processing helix chain 'E' and resid 829 through 852 Processing helix chain 'E' and resid 855 through 857 No H-bonds generated for 'chain 'E' and resid 855 through 857' Processing helix chain 'E' and resid 858 through 865 Processing helix chain 'E' and resid 865 through 872 Processing helix chain 'E' and resid 873 through 877 Processing helix chain 'E' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'C' and resid 739 through 741 Processing sheet with id=AA3, first strand: chain 'E' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'E' and resid 739 through 741 574 hydrogen bonds defined for protein. 1653 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: 1.14 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.43: 2442 1.43 - 1.56: 5328 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9158 Sorted by residual: bond pdb=" C1A PIO E1002 " pdb=" O2C PIO E1002 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1A PIO C1002 " pdb=" O2C PIO C1002 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1B PIO C1002 " pdb=" O3C PIO C1002 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1B PIO E1002 " pdb=" O3C PIO E1002 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O4 PIO C1002 " pdb=" P4 PIO C1002 " ideal model delta sigma weight residual 1.710 1.649 0.061 2.00e-02 2.50e+03 9.30e+00 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 12307 2.43 - 4.87: 111 4.87 - 7.30: 34 7.30 - 9.73: 6 9.73 - 12.16: 4 Bond angle restraints: 12462 Sorted by residual: angle pdb=" O1 PIO E1002 " pdb=" P1 PIO E1002 " pdb=" O13 PIO E1002 " ideal model delta sigma weight residual 97.64 109.80 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O1 PIO C1002 " pdb=" P1 PIO C1002 " pdb=" O13 PIO C1002 " ideal model delta sigma weight residual 97.64 109.62 -11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O11 PIO E1002 " pdb=" P1 PIO E1002 " pdb=" O12 PIO E1002 " ideal model delta sigma weight residual 121.09 109.34 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 PIO C1002 " pdb=" P1 PIO C1002 " pdb=" O12 PIO C1002 " ideal model delta sigma weight residual 121.09 109.39 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2A PIO E1002 " pdb=" C1A PIO E1002 " pdb=" O2C PIO E1002 " ideal model delta sigma weight residual 110.66 120.09 -9.43 3.00e+00 1.11e-01 9.89e+00 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5045 17.94 - 35.87: 207 35.87 - 53.81: 49 53.81 - 71.75: 8 71.75 - 89.68: 5 Dihedral angle restraints: 5314 sinusoidal: 2112 harmonic: 3202 Sorted by residual: dihedral pdb=" CB ARG C 871 " pdb=" CG ARG C 871 " pdb=" CD ARG C 871 " pdb=" NE ARG C 871 " ideal model delta sinusoidal sigma weight residual 60.00 115.23 -55.23 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N LEU C 718 " pdb=" CA LEU C 718 " pdb=" CB LEU C 718 " pdb=" CG LEU C 718 " ideal model delta sinusoidal sigma weight residual -180.00 -126.08 -53.92 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CB MET C 587 " pdb=" CG MET C 587 " pdb=" SD MET C 587 " pdb=" CE MET C 587 " ideal model delta sinusoidal sigma weight residual 60.00 107.91 -47.91 3 1.50e+01 4.44e-03 8.56e+00 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 885 0.025 - 0.050: 334 0.050 - 0.075: 178 0.075 - 0.101: 67 0.101 - 0.126: 40 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 6.21e-01 chirality pdb=" CA ILE E 516 " pdb=" N ILE E 516 " pdb=" C ILE E 516 " pdb=" CB ILE E 516 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL E 828 " pdb=" N VAL E 828 " pdb=" C VAL E 828 " pdb=" CB VAL E 828 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO C 391 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO E 391 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 466 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 467 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 467 " -0.025 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 346 2.73 - 3.27: 9146 3.27 - 3.81: 15090 3.81 - 4.36: 18152 4.36 - 4.90: 31113 Nonbonded interactions: 73847 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.228 3.040 nonbonded pdb=" O VAL C 850 " pdb=" OG1 THR C 853 " model vdw 2.283 3.040 nonbonded pdb=" O LEU C 427 " pdb=" OG1 THR C 431 " model vdw 2.287 3.040 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.324 3.040 ... (remaining 73842 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 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.170 Find NCS groups from input model: 0.100 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.069 9162 Z= 0.171 Angle : 0.666 12.164 12474 Z= 0.309 Chirality : 0.039 0.126 1504 Planarity : 0.005 0.062 1494 Dihedral : 11.001 89.685 3250 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.16 % Allowed : 4.84 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.59 (0.24), residues: 1102 helix: 1.56 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.11 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 387 TYR 0.012 0.001 TYR E 519 PHE 0.008 0.001 PHE C 511 TRP 0.006 0.001 TRP C 831 HIS 0.002 0.000 HIS E 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 ( 9158) covalent geometry : angle 0.66528 / 0.31 (12462) hydrogen bonds : bond 0.16420 / 10.98 ( 574) hydrogen bonds : angle 5.00870 / 3.64 ( 1653) link_BETA1-4 : bond 0.00608 / 0.36 ( 2) link_BETA1-4 : angle 1.16283 / 0.62 ( 6) link_NAG-ASN : bond 0.00258 / 0.15 ( 2) link_NAG-ASN : angle 0.59594 / 0.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 435 MET cc_start: 0.7818 (mtm) cc_final: 0.7610 (mtp) REVERT: C 586 MET cc_start: 0.8579 (mmm) cc_final: 0.8374 (mmt) REVERT: C 622 PHE cc_start: 0.8271 (t80) cc_final: 0.8017 (t80) REVERT: C 626 ASP cc_start: 0.6111 (m-30) cc_final: 0.5832 (m-30) REVERT: C 646 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7412 (ppp80) REVERT: C 676 ILE cc_start: 0.8210 (mt) cc_final: 0.7958 (pt) REVERT: C 812 LEU cc_start: 0.8865 (mt) cc_final: 0.8650 (mp) REVERT: C 885 CYS cc_start: 0.8219 (m) cc_final: 0.7875 (m) REVERT: E 454 LEU cc_start: 0.7955 (mt) cc_final: 0.7689 (mp) REVERT: E 646 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.5647 (ppp80) REVERT: E 650 ILE cc_start: 0.8147 (mp) cc_final: 0.7694 (mt) REVERT: E 759 GLN cc_start: 0.8260 (pp30) cc_final: 0.7957 (pp30) outliers start: 11 outliers final: 2 residues processed: 197 average time/residue: 0.0812 time to fit residues: 21.8852 Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 85 HIS D 82 GLN C 377 GLN C 404 GLN C 630 GLN C 651 HIS C 683 GLN E 377 GLN E 434 GLN E 630 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 804 GLN ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.163887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.140388 restraints weight = 10315.868| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.65 r_work: 0.3358 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9162 Z= 0.114 Angle : 0.495 5.210 12474 Z= 0.248 Chirality : 0.040 0.193 1504 Planarity : 0.005 0.053 1494 Dihedral : 7.533 69.590 1253 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.00 % Allowed : 8.11 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.13 (0.25), residues: 1102 helix: 2.00 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.23 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 760 TYR 0.012 0.001 TYR E 486 PHE 0.011 0.001 PHE E 511 TRP 0.010 0.001 TRP E 492 HIS 0.002 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 9158) covalent geometry : angle 0.49440 / 0.25 (12462) hydrogen bonds : bond 0.04419 / 3.02 ( 574) hydrogen bonds : angle 4.15012 / 3.04 ( 1653) link_BETA1-4 : bond 0.00267 / 0.16 ( 2) link_BETA1-4 : angle 0.64094 / 0.34 ( 6) link_NAG-ASN : bond 0.00118 / 0.07 ( 2) link_NAG-ASN : angle 0.83503 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: C 435 MET cc_start: 0.7937 (mtm) cc_final: 0.7611 (mtp) REVERT: C 622 PHE cc_start: 0.8347 (t80) cc_final: 0.8107 (t80) REVERT: C 626 ASP cc_start: 0.5941 (m-30) cc_final: 0.5731 (m-30) REVERT: C 646 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.6910 (ppp80) REVERT: C 676 ILE cc_start: 0.8163 (mt) cc_final: 0.7952 (pt) REVERT: C 759 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7583 (pp30) REVERT: C 885 CYS cc_start: 0.8617 (m) cc_final: 0.8271 (m) REVERT: E 430 LYS cc_start: 0.6575 (mttp) cc_final: 0.6208 (mttp) REVERT: E 473 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6672 (mm-30) REVERT: E 646 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.6793 (ppp80) REVERT: E 650 ILE cc_start: 0.8090 (mp) cc_final: 0.7665 (mt) REVERT: E 759 GLN cc_start: 0.8356 (pp30) cc_final: 0.7857 (pp30) outliers start: 19 outliers final: 6 residues processed: 157 average time/residue: 0.0722 time to fit residues: 16.0963 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 831 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.157985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.134277 restraints weight = 10333.344| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.64 r_work: 0.3287 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9162 Z= 0.165 Angle : 0.532 5.512 12474 Z= 0.266 Chirality : 0.042 0.189 1504 Planarity : 0.005 0.049 1494 Dihedral : 7.624 72.421 1251 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 8.84 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -0.08 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 760 TYR 0.014 0.002 TYR C 824 PHE 0.014 0.002 PHE E 471 TRP 0.013 0.002 TRP C 492 HIS 0.005 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 9158) covalent geometry : angle 0.53119 / 0.27 (12462) hydrogen bonds : bond 0.04621 / 3.15 ( 574) hydrogen bonds : angle 4.14145 / 3.05 ( 1653) link_BETA1-4 : bond 0.00361 / 0.21 ( 2) link_BETA1-4 : angle 0.87591 / 0.42 ( 6) link_NAG-ASN : bond 0.00168 / 0.10 ( 2) link_NAG-ASN : angle 1.17286 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: C 622 PHE cc_start: 0.8424 (t80) cc_final: 0.8201 (t80) REVERT: C 626 ASP cc_start: 0.6054 (m-30) cc_final: 0.5834 (m-30) REVERT: C 646 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7065 (ppp80) REVERT: C 651 HIS cc_start: 0.6146 (OUTLIER) cc_final: 0.5653 (t70) REVERT: C 676 ILE cc_start: 0.8226 (mt) cc_final: 0.7989 (pt) REVERT: C 759 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7423 (pp30) REVERT: C 884 GLN cc_start: 0.8589 (mt0) cc_final: 0.8302 (mm110) REVERT: C 885 CYS cc_start: 0.8530 (m) cc_final: 0.8186 (m) REVERT: E 399 ASP cc_start: 0.6568 (t0) cc_final: 0.6173 (t0) REVERT: E 430 LYS cc_start: 0.6749 (mttp) cc_final: 0.6401 (mttp) REVERT: E 473 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: E 646 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.5440 (ppp80) REVERT: E 650 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7773 (mt) REVERT: E 759 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7842 (pp30) outliers start: 26 outliers final: 13 residues processed: 159 average time/residue: 0.0709 time to fit residues: 15.9898 Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 831 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 404 GLN C 651 HIS E 521 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.160597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.136663 restraints weight = 10361.116| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.69 r_work: 0.3317 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9162 Z= 0.105 Angle : 0.477 5.393 12474 Z= 0.238 Chirality : 0.040 0.142 1504 Planarity : 0.004 0.049 1494 Dihedral : 7.409 72.481 1251 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.32 % Allowed : 10.53 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.04 (0.25), residues: 1102 helix: 2.09 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -0.12 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 760 TYR 0.013 0.001 TYR E 486 PHE 0.013 0.001 PHE E 471 TRP 0.011 0.001 TRP E 492 HIS 0.007 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 9158) covalent geometry : angle 0.47649 / 0.24 (12462) hydrogen bonds : bond 0.03936 / 2.71 ( 574) hydrogen bonds : angle 4.04360 / 2.98 ( 1653) link_BETA1-4 : bond 0.00354 / 0.21 ( 2) link_BETA1-4 : angle 0.75807 / 0.40 ( 6) link_NAG-ASN : bond 0.00104 / 0.06 ( 2) link_NAG-ASN : angle 0.88132 / 0.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: C 622 PHE cc_start: 0.8416 (t80) cc_final: 0.8152 (t80) REVERT: C 624 ILE cc_start: 0.8059 (mp) cc_final: 0.7845 (mt) REVERT: C 626 ASP cc_start: 0.6041 (m-30) cc_final: 0.5838 (m-30) REVERT: C 646 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7054 (ppp80) REVERT: C 650 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7619 (mp) REVERT: C 676 ILE cc_start: 0.8210 (mt) cc_final: 0.8005 (pt) REVERT: C 885 CYS cc_start: 0.8591 (m) cc_final: 0.8250 (m) REVERT: E 399 ASP cc_start: 0.6592 (t0) cc_final: 0.6058 (t0) REVERT: E 430 LYS cc_start: 0.6708 (mttp) cc_final: 0.6363 (mttp) REVERT: E 473 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: E 646 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.5344 (ppp80) REVERT: E 672 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7578 (tt) REVERT: E 759 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7837 (pp30) REVERT: E 842 ILE cc_start: 0.7902 (mt) cc_final: 0.7671 (tt) outliers start: 22 outliers final: 10 residues processed: 146 average time/residue: 0.0672 time to fit residues: 14.1762 Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 404 GLN C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.154053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.130248 restraints weight = 10460.361| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.64 r_work: 0.3229 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9162 Z= 0.212 Angle : 0.590 6.037 12474 Z= 0.294 Chirality : 0.044 0.156 1504 Planarity : 0.005 0.047 1494 Dihedral : 7.581 73.237 1251 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.47 % Allowed : 10.63 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.52 (0.24), residues: 1102 helix: 1.74 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 388 TYR 0.013 0.002 TYR C 824 PHE 0.015 0.002 PHE E 471 TRP 0.016 0.002 TRP E 492 HIS 0.006 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.21 ( 9158) covalent geometry : angle 0.58893 / 0.29 (12462) hydrogen bonds : bond 0.05002 / 3.43 ( 574) hydrogen bonds : angle 4.28437 / 3.16 ( 1653) link_BETA1-4 : bond 0.00350 / 0.20 ( 2) link_BETA1-4 : angle 1.05917 / 0.47 ( 6) link_NAG-ASN : bond 0.00276 / 0.15 ( 2) link_NAG-ASN : angle 1.44763 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.283 Fit side-chains REVERT: C 622 PHE cc_start: 0.8462 (t80) cc_final: 0.8165 (t80) REVERT: C 646 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.6200 (ppp80) REVERT: C 651 HIS cc_start: 0.5995 (OUTLIER) cc_final: 0.5526 (t70) REVERT: C 676 ILE cc_start: 0.8244 (mt) cc_final: 0.7950 (pt) REVERT: C 884 GLN cc_start: 0.8626 (mt0) cc_final: 0.8395 (mm110) REVERT: C 885 CYS cc_start: 0.8585 (m) cc_final: 0.8243 (m) REVERT: E 399 ASP cc_start: 0.6848 (t0) cc_final: 0.6520 (t0) REVERT: E 430 LYS cc_start: 0.6790 (mttp) cc_final: 0.6415 (mttp) REVERT: E 473 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6717 (mm-30) REVERT: E 646 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.5606 (ppp80) REVERT: E 650 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7779 (mp) REVERT: E 672 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7729 (tt) REVERT: E 759 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7837 (pp30) REVERT: E 777 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6632 (tm-30) outliers start: 33 outliers final: 17 residues processed: 153 average time/residue: 0.0725 time to fit residues: 15.8439 Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.131386 restraints weight = 10340.800| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.62 r_work: 0.3243 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9162 Z= 0.184 Angle : 0.548 5.752 12474 Z= 0.274 Chirality : 0.042 0.150 1504 Planarity : 0.005 0.047 1494 Dihedral : 7.527 73.848 1251 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.84 % Allowed : 11.37 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.24), residues: 1102 helix: 1.76 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -0.47 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 760 TYR 0.013 0.002 TYR E 824 PHE 0.015 0.001 PHE E 471 TRP 0.015 0.002 TRP E 492 HIS 0.009 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 ( 9158) covalent geometry : angle 0.54749 / 0.27 (12462) hydrogen bonds : bond 0.04702 / 3.23 ( 574) hydrogen bonds : angle 4.24249 / 3.12 ( 1653) link_BETA1-4 : bond 0.00400 / 0.24 ( 2) link_BETA1-4 : angle 0.91070 / 0.42 ( 6) link_NAG-ASN : bond 0.00158 / 0.09 ( 2) link_NAG-ASN : angle 1.32846 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: C 622 PHE cc_start: 0.8504 (t80) cc_final: 0.8208 (t80) REVERT: C 646 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6225 (ppp80) REVERT: C 651 HIS cc_start: 0.5859 (OUTLIER) cc_final: 0.5375 (t70) REVERT: C 676 ILE cc_start: 0.8215 (mt) cc_final: 0.7945 (pt) REVERT: C 755 GLU cc_start: 0.7757 (pt0) cc_final: 0.7395 (pt0) REVERT: C 884 GLN cc_start: 0.8602 (mt0) cc_final: 0.8372 (mm110) REVERT: E 399 ASP cc_start: 0.6897 (t0) cc_final: 0.6554 (t0) REVERT: E 430 LYS cc_start: 0.6801 (mttp) cc_final: 0.6421 (mttp) REVERT: E 473 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: E 646 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.5650 (ppp80) REVERT: E 650 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7750 (mp) REVERT: E 672 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7705 (tt) REVERT: E 759 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7816 (pp30) REVERT: E 777 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6648 (tm-30) outliers start: 27 outliers final: 16 residues processed: 152 average time/residue: 0.0803 time to fit residues: 17.4580 Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 640 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS E 569 ASN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.158096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134036 restraints weight = 10281.790| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.56 r_work: 0.3289 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9162 Z= 0.107 Angle : 0.480 5.433 12474 Z= 0.241 Chirality : 0.040 0.140 1504 Planarity : 0.004 0.050 1494 Dihedral : 7.254 74.030 1251 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.74 % Allowed : 12.32 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1102 helix: 2.04 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -0.36 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 760 TYR 0.012 0.001 TYR C 486 PHE 0.013 0.001 PHE E 471 TRP 0.014 0.001 TRP E 492 HIS 0.021 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9158) covalent geometry : angle 0.47933 / 0.24 (12462) hydrogen bonds : bond 0.03960 / 2.74 ( 574) hydrogen bonds : angle 4.06663 / 3.00 ( 1653) link_BETA1-4 : bond 0.00379 / 0.22 ( 2) link_BETA1-4 : angle 0.76299 / 0.40 ( 6) link_NAG-ASN : bond 0.00110 / 0.07 ( 2) link_NAG-ASN : angle 0.95350 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 622 PHE cc_start: 0.8450 (t80) cc_final: 0.8142 (t80) REVERT: C 624 ILE cc_start: 0.8098 (mp) cc_final: 0.7831 (mp) REVERT: C 646 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.6238 (ppp80) REVERT: C 651 HIS cc_start: 0.5769 (OUTLIER) cc_final: 0.5084 (t70) REVERT: C 676 ILE cc_start: 0.8195 (mt) cc_final: 0.7967 (pt) REVERT: C 755 GLU cc_start: 0.7736 (pt0) cc_final: 0.7397 (pt0) REVERT: C 884 GLN cc_start: 0.8543 (mt0) cc_final: 0.8286 (mm110) REVERT: E 399 ASP cc_start: 0.6908 (t0) cc_final: 0.6589 (t0) REVERT: E 430 LYS cc_start: 0.6750 (mttp) cc_final: 0.6393 (mttp) REVERT: E 432 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.7012 (mpt180) REVERT: E 473 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: E 646 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.5592 (ppp80) REVERT: E 650 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7579 (mp) REVERT: E 672 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7658 (tt) REVERT: E 759 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: E 777 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6636 (tm-30) REVERT: E 842 ILE cc_start: 0.7870 (mt) cc_final: 0.7667 (tt) outliers start: 26 outliers final: 15 residues processed: 153 average time/residue: 0.0809 time to fit residues: 17.7196 Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.158783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.134414 restraints weight = 10244.838| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.58 r_work: 0.3286 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9162 Z= 0.111 Angle : 0.481 5.867 12474 Z= 0.242 Chirality : 0.040 0.138 1504 Planarity : 0.004 0.050 1494 Dihedral : 7.151 73.342 1251 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.95 % Allowed : 11.89 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.93 (0.25), residues: 1102 helix: 2.09 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -0.39 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 760 TYR 0.011 0.001 TYR C 486 PHE 0.013 0.001 PHE E 471 TRP 0.013 0.001 TRP E 492 HIS 0.003 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9158) covalent geometry : angle 0.48047 / 0.24 (12462) hydrogen bonds : bond 0.03896 / 2.70 ( 574) hydrogen bonds : angle 4.03240 / 2.97 ( 1653) link_BETA1-4 : bond 0.00380 / 0.22 ( 2) link_BETA1-4 : angle 0.77721 / 0.40 ( 6) link_NAG-ASN : bond 0.00103 / 0.06 ( 2) link_NAG-ASN : angle 0.96326 / 0.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7427 (mmm160) REVERT: C 622 PHE cc_start: 0.8454 (t80) cc_final: 0.8125 (t80) REVERT: C 624 ILE cc_start: 0.8090 (mp) cc_final: 0.7817 (mp) REVERT: C 646 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6187 (ppp80) REVERT: C 651 HIS cc_start: 0.5532 (OUTLIER) cc_final: 0.4442 (t-90) REVERT: C 676 ILE cc_start: 0.8196 (mt) cc_final: 0.7968 (pt) REVERT: C 755 GLU cc_start: 0.7762 (pt0) cc_final: 0.7393 (pt0) REVERT: C 884 GLN cc_start: 0.8545 (mt0) cc_final: 0.8271 (mm110) REVERT: E 399 ASP cc_start: 0.6908 (t0) cc_final: 0.6581 (t0) REVERT: E 430 LYS cc_start: 0.6741 (mttp) cc_final: 0.6414 (mttp) REVERT: E 432 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7016 (mpt180) REVERT: E 473 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: E 646 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.5496 (ppp80) REVERT: E 650 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7569 (mp) REVERT: E 672 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7651 (tt) REVERT: E 759 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7786 (pp30) REVERT: E 777 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6636 (tm-30) REVERT: E 842 ILE cc_start: 0.7863 (mt) cc_final: 0.7625 (tt) outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 0.0883 time to fit residues: 19.1403 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.157328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.133361 restraints weight = 10361.956| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.54 r_work: 0.3280 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9162 Z= 0.143 Angle : 0.507 5.856 12474 Z= 0.255 Chirality : 0.041 0.139 1504 Planarity : 0.005 0.047 1494 Dihedral : 7.177 72.824 1251 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.95 % Allowed : 11.89 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.85 (0.25), residues: 1102 helix: 1.98 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.30 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 760 TYR 0.010 0.001 TYR C 824 PHE 0.013 0.001 PHE E 471 TRP 0.014 0.001 TRP E 492 HIS 0.004 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 9158) covalent geometry : angle 0.50613 / 0.25 (12462) hydrogen bonds : bond 0.04117 / 2.84 ( 574) hydrogen bonds : angle 4.07829 / 3.00 ( 1653) link_BETA1-4 : bond 0.00383 / 0.22 ( 2) link_BETA1-4 : angle 0.79592 / 0.39 ( 6) link_NAG-ASN : bond 0.00087 / 0.05 ( 2) link_NAG-ASN : angle 1.09933 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 622 PHE cc_start: 0.8458 (t80) cc_final: 0.8144 (t80) REVERT: C 624 ILE cc_start: 0.8087 (mp) cc_final: 0.7812 (mp) REVERT: C 646 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.6165 (ppp80) REVERT: C 651 HIS cc_start: 0.5694 (OUTLIER) cc_final: 0.5319 (t70) REVERT: C 676 ILE cc_start: 0.8203 (mt) cc_final: 0.7960 (pt) REVERT: C 755 GLU cc_start: 0.7738 (pt0) cc_final: 0.7375 (pt0) REVERT: C 884 GLN cc_start: 0.8549 (mt0) cc_final: 0.8276 (mm110) REVERT: E 399 ASP cc_start: 0.6937 (t0) cc_final: 0.6577 (t0) REVERT: E 430 LYS cc_start: 0.6742 (mttp) cc_final: 0.6393 (mttp) REVERT: E 432 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7036 (mpt180) REVERT: E 473 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6563 (mm-30) REVERT: E 646 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.5504 (ppp80) REVERT: E 650 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7632 (mp) REVERT: E 672 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7656 (tt) REVERT: E 759 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7815 (pp30) REVERT: E 777 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6640 (tm-30) REVERT: E 842 ILE cc_start: 0.7860 (mt) cc_final: 0.7626 (tt) outliers start: 28 outliers final: 20 residues processed: 152 average time/residue: 0.0901 time to fit residues: 19.4852 Evaluate side-chains 159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.159254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135164 restraints weight = 10259.517| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.56 r_work: 0.3302 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9162 Z= 0.110 Angle : 0.491 6.963 12474 Z= 0.247 Chirality : 0.040 0.133 1504 Planarity : 0.005 0.091 1494 Dihedral : 7.087 73.001 1251 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.53 % Allowed : 12.32 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.97 (0.25), residues: 1102 helix: 2.09 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.30 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 760 TYR 0.011 0.001 TYR C 486 PHE 0.013 0.001 PHE E 471 TRP 0.014 0.001 TRP E 492 HIS 0.008 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9158) covalent geometry : angle 0.49031 / 0.25 (12462) hydrogen bonds : bond 0.03837 / 2.66 ( 574) hydrogen bonds : angle 4.02229 / 2.96 ( 1653) link_BETA1-4 : bond 0.00379 / 0.22 ( 2) link_BETA1-4 : angle 0.77627 / 0.40 ( 6) link_NAG-ASN : bond 0.00115 / 0.07 ( 2) link_NAG-ASN : angle 0.93215 / 0.55 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: C 622 PHE cc_start: 0.8468 (t80) cc_final: 0.8159 (t80) REVERT: C 624 ILE cc_start: 0.8074 (mp) cc_final: 0.7836 (mp) REVERT: C 646 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.6134 (ppp80) REVERT: C 676 ILE cc_start: 0.8232 (mt) cc_final: 0.8015 (pt) REVERT: C 755 GLU cc_start: 0.7724 (pt0) cc_final: 0.7341 (pt0) REVERT: C 884 GLN cc_start: 0.8539 (mt0) cc_final: 0.8261 (mm110) REVERT: E 399 ASP cc_start: 0.6941 (t0) cc_final: 0.6590 (t0) REVERT: E 430 LYS cc_start: 0.6691 (mttp) cc_final: 0.6357 (mttp) REVERT: E 432 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.7031 (mpt180) REVERT: E 473 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6571 (mm-30) REVERT: E 646 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.5486 (ppp80) REVERT: E 650 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7758 (mt) REVERT: E 672 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7636 (tt) REVERT: E 759 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7816 (pp30) REVERT: E 777 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6636 (tm-30) REVERT: E 842 ILE cc_start: 0.7856 (mt) cc_final: 0.7632 (tt) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.0939 time to fit residues: 19.6515 Evaluate side-chains 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 708 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 811 LEU Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 0.0470 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 77 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.160088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136231 restraints weight = 10148.455| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.55 r_work: 0.3315 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9162 Z= 0.102 Angle : 0.476 5.623 12474 Z= 0.240 Chirality : 0.039 0.131 1504 Planarity : 0.004 0.058 1494 Dihedral : 7.000 72.550 1251 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.53 % Allowed : 12.63 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.05 (0.25), residues: 1102 helix: 2.14 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 760 TYR 0.012 0.001 TYR C 486 PHE 0.013 0.001 PHE E 471 TRP 0.014 0.001 TRP E 492 HIS 0.004 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9158) covalent geometry : angle 0.47542 / 0.24 (12462) hydrogen bonds : bond 0.03693 / 2.56 ( 574) hydrogen bonds : angle 3.98186 / 2.94 ( 1653) link_BETA1-4 : bond 0.00382 / 0.23 ( 2) link_BETA1-4 : angle 0.78480 / 0.41 ( 6) link_NAG-ASN : bond 0.00124 / 0.08 ( 2) link_NAG-ASN : angle 0.88290 / 0.52 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.43 seconds wall clock time: 45 minutes 59.89 seconds (2759.89 seconds total)