Starting phenix.real_space_refine on Thu Jul 2 14:09:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.cif" model { file = "/net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crq_26955/07_2026/8crq_26955.cif" } resolution = 3.2 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= 0.122 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 24 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: 2.07, per 1000 atoms: 0.23 Number of scatterers: 8936 At special positions: 0 Unit cell: (142.76, 80.925, 110.39, 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: 1.05 Conformation dependent library (CDL) restraints added in 363.7 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: 63 helices and 4 sheets defined 75.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 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 432 removed outlier: 3.523A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.563A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 516 Processing helix chain 'C' and resid 517 through 547 removed outlier: 3.657A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.678A 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 660 through 667 removed outlier: 3.809A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.672A 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 701 through 719 removed outlier: 3.723A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.816A 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: 3.826A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 813 through 814 No H-bonds generated for 'chain 'C' and resid 813 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: 3.521A 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: 3.613A 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: 3.712A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.712A pdb=" N VAL E 513 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 547 removed outlier: 3.606A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 594 removed outlier: 3.716A 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: 3.720A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.546A 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 718 removed outlier: 3.594A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (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 773 through 775 No H-bonds generated for 'chain 'E' and resid 773 through 775' Processing helix chain 'E' and resid 776 through 781 Processing helix chain 'E' and resid 784 through 799 removed outlier: 3.755A 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 removed outlier: 3.508A pdb=" N HIS E 819 " --> pdb=" O PRO E 816 " (cutoff:3.500A) 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 removed outlier: 3.536A pdb=" N LEU E 869 " --> pdb=" O LEU E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 878 removed outlier: 3.740A pdb=" N LEU E 876 " --> pdb=" O VAL E 872 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 877 " --> pdb=" O LEU E 873 " (cutoff:3.500A) 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 741 576 hydrogen bonds defined for protein. 1662 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: 1.41 Time building geometry restraints manager: 1.22 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: 2435 1.43 - 1.56: 5335 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 1.400 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1B PIO E1002 " pdb=" O3C PIO E1002 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1A PIO C1002 " pdb=" O2C PIO C1002 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1B PIO C1002 " pdb=" O3C PIO C1002 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O4 PIO E1002 " pdb=" P4 PIO E1002 " ideal model delta sigma weight residual 1.710 1.646 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12296 2.48 - 4.96: 125 4.96 - 7.45: 31 7.45 - 9.93: 5 9.93 - 12.41: 5 Bond angle restraints: 12462 Sorted by residual: angle pdb=" O1 PIO C1002 " pdb=" P1 PIO C1002 " pdb=" O13 PIO C1002 " ideal model delta sigma weight residual 97.64 110.05 -12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" O1 PIO E1002 " pdb=" P1 PIO E1002 " pdb=" O13 PIO E1002 " ideal model delta sigma weight residual 97.64 109.74 -12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O11 PIO C1002 " pdb=" P1 PIO C1002 " pdb=" O12 PIO C1002 " ideal model delta sigma weight residual 121.09 109.25 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" O11 PIO E1002 " pdb=" P1 PIO E1002 " pdb=" O12 PIO E1002 " ideal model delta sigma weight residual 121.09 109.66 11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C2A PIO E1002 " pdb=" C1A PIO E1002 " pdb=" O2C PIO E1002 " ideal model delta sigma weight residual 110.66 120.87 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4997 17.91 - 35.83: 257 35.83 - 53.74: 45 53.74 - 71.66: 12 71.66 - 89.57: 3 Dihedral angle restraints: 5314 sinusoidal: 2112 harmonic: 3202 Sorted by residual: dihedral pdb=" CA GLN C 434 " pdb=" C GLN C 434 " pdb=" N MET C 435 " pdb=" CA MET C 435 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PRO C 722 " pdb=" C PRO C 722 " pdb=" N TRP C 723 " pdb=" CA TRP C 723 " ideal model delta harmonic sigma weight residual 180.00 164.57 15.43 0 5.00e+00 4.00e-02 9.53e+00 dihedral pdb=" CB ARG E 879 " pdb=" CG ARG E 879 " pdb=" CD ARG E 879 " pdb=" NE ARG E 879 " ideal model delta sinusoidal sigma weight residual 60.00 118.22 -58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1061 0.041 - 0.082: 348 0.082 - 0.123: 88 0.123 - 0.164: 5 0.164 - 0.205: 2 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CB ILE E 487 " pdb=" CA ILE E 487 " pdb=" CG1 ILE E 487 " pdb=" CG2 ILE E 487 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE C 487 " pdb=" CA ILE C 487 " pdb=" CG1 ILE C 487 " pdb=" CG2 ILE C 487 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" C2C PIO E1002 " pdb=" C1C PIO E1002 " pdb=" C3C PIO E1002 " pdb=" O2C PIO E1002 " both_signs ideal model delta sigma weight residual False -2.56 -2.40 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " -0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO E 391 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+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 GLY E 466 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO E 467 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 467 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 467 " -0.026 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 205 2.71 - 3.26: 9079 3.26 - 3.81: 14819 3.81 - 4.35: 18594 4.35 - 4.90: 31446 Nonbonded interactions: 74143 Sorted by model distance: nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.222 3.040 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR C 393 " pdb=" O LEU C 453 " model vdw 2.304 3.040 nonbonded pdb=" O LEU C 863 " pdb=" OG1 THR C 866 " model vdw 2.310 3.040 ... (remaining 74138 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 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: 0.600 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.140 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.004 0.068 9162 Z= 0.194 Angle : 0.717 12.411 12474 Z= 0.340 Chirality : 0.042 0.205 1504 Planarity : 0.006 0.063 1494 Dihedral : 11.492 89.570 3250 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.37 % Allowed : 4.63 % 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: 1.20 (0.24), residues: 1102 helix: 1.20 (0.18), residues: 760 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 387 TYR 0.017 0.002 TYR C 519 PHE 0.013 0.001 PHE E 471 TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 9158) covalent geometry : angle 0.71670 / 0.34 (12462) hydrogen bonds : bond 0.15701 / 10.38 ( 576) hydrogen bonds : angle 5.23809 / 3.89 ( 1662) link_BETA1-4 : bond 0.00631 / 0.36 ( 2) link_BETA1-4 : angle 1.59014 / 0.78 ( 6) link_NAG-ASN : bond 0.00040 / 0.02 ( 2) link_NAG-ASN : angle 0.83717 / 0.46 ( 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 213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.331 Fit side-chains REVERT: B 92 ILE cc_start: 0.7136 (tp) cc_final: 0.6879 (tp) REVERT: C 487 ILE cc_start: 0.8281 (tp) cc_final: 0.7785 (tp) REVERT: C 646 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.6014 (ppp80) REVERT: C 693 GLU cc_start: 0.8381 (pm20) cc_final: 0.8160 (pm20) REVERT: C 757 LYS cc_start: 0.8474 (mmtp) cc_final: 0.8252 (mmtt) REVERT: C 782 ARG cc_start: 0.7842 (mtp85) cc_final: 0.6798 (ptt90) REVERT: C 827 ARG cc_start: 0.7075 (mtp85) cc_final: 0.6698 (mmm160) REVERT: E 511 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7802 (p90) REVERT: E 514 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7906 (ptp-110) REVERT: E 589 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7758 (ttt90) REVERT: E 617 MET cc_start: 0.8229 (mmm) cc_final: 0.7917 (mmt) REVERT: E 621 ASP cc_start: 0.9119 (t70) cc_final: 0.8796 (t0) REVERT: E 646 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6855 (ppp80) REVERT: E 663 MET cc_start: 0.5526 (tpt) cc_final: 0.4561 (tpp) REVERT: E 782 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7699 (mpt180) outliers start: 13 outliers final: 5 residues processed: 211 average time/residue: 0.1114 time to fit residues: 31.4301 Evaluate side-chains 174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 560 VAL 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: 0.1980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN D 82 GLN C 377 GLN C 569 ASN C 630 GLN C 683 GLN E 377 GLN E 564 GLN E 630 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.153810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129261 restraints weight = 10563.941| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.50 r_work: 0.3250 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9162 Z= 0.117 Angle : 0.512 5.228 12474 Z= 0.259 Chirality : 0.041 0.175 1504 Planarity : 0.005 0.057 1494 Dihedral : 7.891 82.580 1257 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.89 % Allowed : 9.05 % Favored : 89.05 % 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: 2.07 (0.25), residues: 1102 helix: 2.03 (0.19), residues: 732 sheet: None (None), residues: 0 loop : 0.11 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 656 TYR 0.015 0.001 TYR E 486 PHE 0.025 0.001 PHE E 476 TRP 0.025 0.002 TRP C 492 HIS 0.001 0.000 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9158) covalent geometry : angle 0.51118 / 0.26 (12462) hydrogen bonds : bond 0.04303 / 2.91 ( 576) hydrogen bonds : angle 4.29039 / 3.18 ( 1662) link_BETA1-4 : bond 0.00541 / 0.31 ( 2) link_BETA1-4 : angle 0.89604 / 0.44 ( 6) link_NAG-ASN : bond 0.00247 / 0.14 ( 2) link_NAG-ASN : angle 0.86002 / 0.49 ( 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 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.321 Fit side-chains REVERT: C 427 LEU cc_start: 0.8020 (tp) cc_final: 0.7807 (tt) REVERT: C 646 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.5543 (ppp80) REVERT: C 782 ARG cc_start: 0.8142 (mtp85) cc_final: 0.6728 (ptt90) REVERT: C 807 ASP cc_start: 0.6921 (m-30) cc_final: 0.6665 (m-30) REVERT: C 827 ARG cc_start: 0.7139 (mtp85) cc_final: 0.6819 (mmm160) REVERT: E 372 LEU cc_start: 0.7971 (mt) cc_final: 0.7721 (mt) REVERT: E 503 LEU cc_start: 0.8343 (mt) cc_final: 0.8091 (mp) REVERT: E 511 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7702 (p90) REVERT: E 514 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7702 (ptp-110) REVERT: E 539 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8159 (mtpp) REVERT: E 589 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7589 (ttt90) REVERT: E 593 ASN cc_start: 0.8258 (m110) cc_final: 0.8016 (m110) REVERT: E 617 MET cc_start: 0.8145 (mmm) cc_final: 0.7923 (mmt) REVERT: E 621 ASP cc_start: 0.9149 (t70) cc_final: 0.8906 (t0) REVERT: E 663 MET cc_start: 0.5251 (tpt) cc_final: 0.4331 (tpp) REVERT: E 676 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7947 (mp) REVERT: E 782 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7706 (mpt180) outliers start: 18 outliers final: 13 residues processed: 178 average time/residue: 0.1144 time to fit residues: 27.3578 Evaluate side-chains 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU 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 649 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.0040 chunk 108 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 0.0670 chunk 60 optimal weight: 9.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 569 ASN E 564 GLN E 651 HIS E 819 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.132063 restraints weight = 10500.753| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.48 r_work: 0.3285 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9162 Z= 0.096 Angle : 0.456 5.123 12474 Z= 0.231 Chirality : 0.040 0.183 1504 Planarity : 0.005 0.053 1494 Dihedral : 7.565 92.579 1257 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.00 % Allowed : 10.00 % Favored : 88.00 % 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: 2.37 (0.25), residues: 1102 helix: 2.25 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 388 TYR 0.020 0.001 TYR E 486 PHE 0.026 0.001 PHE E 476 TRP 0.014 0.001 TRP C 492 HIS 0.002 0.000 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 ( 9158) covalent geometry : angle 0.45566 / 0.23 (12462) hydrogen bonds : bond 0.03530 / 2.42 ( 576) hydrogen bonds : angle 4.04941 / 2.99 ( 1662) link_BETA1-4 : bond 0.00307 / 0.18 ( 2) link_BETA1-4 : angle 0.92601 / 0.49 ( 6) link_NAG-ASN : bond 0.00160 / 0.09 ( 2) link_NAG-ASN : angle 0.91157 / 0.50 ( 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 195 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.292 Fit side-chains REVERT: C 384 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.6461 (ttp-110) REVERT: C 430 LYS cc_start: 0.8238 (ttmm) cc_final: 0.8025 (ttmt) REVERT: C 646 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.5417 (ppp80) REVERT: C 693 GLU cc_start: 0.8462 (pm20) cc_final: 0.8246 (pm20) REVERT: C 782 ARG cc_start: 0.8159 (mtp85) cc_final: 0.6679 (ptt90) REVERT: C 807 ASP cc_start: 0.6901 (m-30) cc_final: 0.6628 (m-30) REVERT: C 827 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6812 (mmm160) REVERT: E 503 LEU cc_start: 0.8315 (mt) cc_final: 0.8008 (mp) REVERT: E 515 PHE cc_start: 0.7728 (m-80) cc_final: 0.7427 (m-80) REVERT: E 589 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7592 (ttt90) REVERT: E 593 ASN cc_start: 0.8263 (m110) cc_final: 0.8020 (m110) REVERT: E 646 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.4735 (ppp80) REVERT: E 663 MET cc_start: 0.5137 (tpt) cc_final: 0.4177 (tpp) REVERT: E 676 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7895 (mp) REVERT: E 782 ARG cc_start: 0.8415 (mtp85) cc_final: 0.7623 (mpt180) outliers start: 19 outliers final: 9 residues processed: 182 average time/residue: 0.1085 time to fit residues: 26.6074 Evaluate side-chains 175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 881 VAL Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 819 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.129591 restraints weight = 10626.228| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.51 r_work: 0.3255 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9162 Z= 0.118 Angle : 0.480 5.199 12474 Z= 0.239 Chirality : 0.041 0.150 1504 Planarity : 0.005 0.052 1494 Dihedral : 6.845 57.146 1250 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.42 % Allowed : 11.47 % Favored : 86.11 % 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: 2.31 (0.25), residues: 1102 helix: 2.21 (0.19), residues: 742 sheet: None (None), residues: 0 loop : 0.16 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 388 TYR 0.016 0.001 TYR E 486 PHE 0.014 0.001 PHE C 471 TRP 0.011 0.001 TRP C 492 HIS 0.002 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9158) covalent geometry : angle 0.47967 / 0.24 (12462) hydrogen bonds : bond 0.03685 / 2.54 ( 576) hydrogen bonds : angle 4.04914 / 2.99 ( 1662) link_BETA1-4 : bond 0.00253 / 0.15 ( 2) link_BETA1-4 : angle 0.90765 / 0.46 ( 6) link_NAG-ASN : bond 0.00121 / 0.07 ( 2) link_NAG-ASN : angle 0.89050 / 0.48 ( 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 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.353 Fit side-chains REVERT: B 83 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7182 (tt) REVERT: C 384 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.6485 (ttp-110) REVERT: C 646 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.5419 (ppp80) REVERT: C 650 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 693 GLU cc_start: 0.8519 (pm20) cc_final: 0.8313 (pm20) REVERT: C 782 ARG cc_start: 0.8165 (mtp85) cc_final: 0.6682 (ptt90) REVERT: C 807 ASP cc_start: 0.6925 (m-30) cc_final: 0.6655 (m-30) REVERT: C 827 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6796 (mmm160) REVERT: E 503 LEU cc_start: 0.8310 (mt) cc_final: 0.7850 (tp) REVERT: E 511 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7699 (p90) REVERT: E 515 PHE cc_start: 0.7717 (m-80) cc_final: 0.7430 (m-80) REVERT: E 589 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7599 (ttt90) REVERT: E 593 ASN cc_start: 0.8266 (m110) cc_final: 0.8045 (m110) REVERT: E 646 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.4997 (ppp80) REVERT: E 650 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7238 (mp) REVERT: E 663 MET cc_start: 0.5142 (tpt) cc_final: 0.4181 (tpp) REVERT: E 676 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7915 (mp) REVERT: E 730 ARG cc_start: 0.8459 (mtm180) cc_final: 0.8190 (mtm180) REVERT: E 782 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7627 (mpt180) outliers start: 23 outliers final: 10 residues processed: 182 average time/residue: 0.1139 time to fit residues: 27.9325 Evaluate side-chains 178 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.0010 chunk 64 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.155025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.131150 restraints weight = 10614.300| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.47 r_work: 0.3273 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9162 Z= 0.102 Angle : 0.463 5.156 12474 Z= 0.231 Chirality : 0.040 0.167 1504 Planarity : 0.005 0.050 1494 Dihedral : 6.735 57.938 1250 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.63 % Allowed : 11.79 % Favored : 85.58 % 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: 2.42 (0.25), residues: 1102 helix: 2.25 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.24 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 388 TYR 0.014 0.001 TYR E 486 PHE 0.016 0.001 PHE E 476 TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 9158) covalent geometry : angle 0.46253 / 0.23 (12462) hydrogen bonds : bond 0.03463 / 2.39 ( 576) hydrogen bonds : angle 3.98587 / 2.95 ( 1662) link_BETA1-4 : bond 0.00204 / 0.11 ( 2) link_BETA1-4 : angle 0.89096 / 0.46 ( 6) link_NAG-ASN : bond 0.00127 / 0.07 ( 2) link_NAG-ASN : angle 0.87908 / 0.47 ( 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 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.354 Fit side-chains REVERT: B 83 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7103 (tt) REVERT: C 646 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.5459 (ppp80) REVERT: C 650 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8397 (mp) REVERT: C 782 ARG cc_start: 0.8162 (mtp85) cc_final: 0.6684 (ptt90) REVERT: C 807 ASP cc_start: 0.6908 (m-30) cc_final: 0.6635 (m-30) REVERT: C 827 ARG cc_start: 0.7162 (mtp85) cc_final: 0.6792 (mmm160) REVERT: E 511 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7687 (p90) REVERT: E 515 PHE cc_start: 0.7657 (m-80) cc_final: 0.7352 (m-80) REVERT: E 589 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7594 (ttt90) REVERT: E 593 ASN cc_start: 0.8238 (m110) cc_final: 0.8020 (m110) REVERT: E 621 ASP cc_start: 0.9166 (t70) cc_final: 0.8934 (t0) REVERT: E 646 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.4888 (ppp80) REVERT: E 650 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7162 (mp) REVERT: E 658 GLU cc_start: 0.7273 (tp30) cc_final: 0.6521 (mp0) REVERT: E 663 MET cc_start: 0.5148 (tpt) cc_final: 0.4187 (tpp) REVERT: E 676 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (mp) REVERT: E 730 ARG cc_start: 0.8413 (mtm180) cc_final: 0.8190 (mtm180) REVERT: E 782 ARG cc_start: 0.8445 (mtp85) cc_final: 0.7689 (mpt180) outliers start: 25 outliers final: 13 residues processed: 189 average time/residue: 0.1133 time to fit residues: 28.8193 Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU 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 650 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL 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: 4.9990 chunk 43 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.152328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128291 restraints weight = 10569.469| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.48 r_work: 0.3237 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9162 Z= 0.139 Angle : 0.504 5.330 12474 Z= 0.250 Chirality : 0.041 0.178 1504 Planarity : 0.005 0.051 1494 Dihedral : 6.837 56.410 1250 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.63 % Allowed : 12.84 % Favored : 84.53 % 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: 2.19 (0.25), residues: 1102 helix: 2.09 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.09 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 384 TYR 0.016 0.001 TYR C 519 PHE 0.013 0.001 PHE C 471 TRP 0.012 0.001 TRP C 492 HIS 0.002 0.001 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9158) covalent geometry : angle 0.50383 / 0.25 (12462) hydrogen bonds : bond 0.03866 / 2.67 ( 576) hydrogen bonds : angle 4.06754 / 3.00 ( 1662) link_BETA1-4 : bond 0.00217 / 0.13 ( 2) link_BETA1-4 : angle 0.93475 / 0.47 ( 6) link_NAG-ASN : bond 0.00085 / 0.05 ( 2) link_NAG-ASN : angle 0.96150 / 0.52 ( 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 196 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.324 Fit side-chains REVERT: B 83 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7102 (tt) REVERT: C 384 ARG cc_start: 0.7442 (ttm-80) cc_final: 0.6528 (ttp-110) REVERT: C 499 LEU cc_start: 0.7749 (tp) cc_final: 0.7354 (tt) REVERT: C 646 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.5452 (ppp80) REVERT: C 650 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8418 (mp) REVERT: C 782 ARG cc_start: 0.8187 (mtp85) cc_final: 0.6707 (ptt90) REVERT: C 807 ASP cc_start: 0.6972 (m-30) cc_final: 0.6707 (m-30) REVERT: E 511 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7753 (p90) REVERT: E 515 PHE cc_start: 0.7695 (m-80) cc_final: 0.7372 (m-80) REVERT: E 589 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7613 (ttt90) REVERT: E 593 ASN cc_start: 0.8247 (m110) cc_final: 0.8029 (m110) REVERT: E 621 ASP cc_start: 0.9164 (t70) cc_final: 0.8935 (t0) REVERT: E 646 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.5095 (ppp80) REVERT: E 650 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7421 (mp) REVERT: E 658 GLU cc_start: 0.7334 (tp30) cc_final: 0.6544 (mp0) REVERT: E 663 MET cc_start: 0.5159 (tpt) cc_final: 0.4169 (tpp) REVERT: E 676 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7970 (mp) REVERT: E 693 GLU cc_start: 0.7659 (pt0) cc_final: 0.7431 (pm20) REVERT: E 730 ARG cc_start: 0.8417 (mtm180) cc_final: 0.8194 (mtm180) REVERT: E 754 GLN cc_start: 0.7319 (tp40) cc_final: 0.7075 (tp40) REVERT: E 782 ARG cc_start: 0.8510 (mtp85) cc_final: 0.7673 (mpt180) outliers start: 25 outliers final: 15 residues processed: 186 average time/residue: 0.1091 time to fit residues: 27.3358 Evaluate side-chains 188 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 487 ILE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL 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: 0.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.154434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.130349 restraints weight = 10590.218| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.49 r_work: 0.3262 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9162 Z= 0.102 Angle : 0.465 5.097 12474 Z= 0.232 Chirality : 0.040 0.151 1504 Planarity : 0.004 0.050 1494 Dihedral : 6.771 57.740 1250 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.53 % Allowed : 13.05 % Favored : 84.42 % 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: 2.34 (0.25), residues: 1102 helix: 2.20 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.16 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 388 TYR 0.013 0.001 TYR C 519 PHE 0.015 0.001 PHE C 471 TRP 0.014 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9158) covalent geometry : angle 0.46393 / 0.23 (12462) hydrogen bonds : bond 0.03470 / 2.40 ( 576) hydrogen bonds : angle 3.98614 / 2.95 ( 1662) link_BETA1-4 : bond 0.00189 / 0.11 ( 2) link_BETA1-4 : angle 0.94803 / 0.49 ( 6) link_NAG-ASN : bond 0.00159 / 0.09 ( 2) link_NAG-ASN : angle 0.88112 / 0.48 ( 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 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.315 Fit side-chains REVERT: B 83 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7054 (tt) REVERT: C 384 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.6411 (ttp-110) REVERT: C 559 MET cc_start: 0.6169 (mmm) cc_final: 0.5195 (ttp) REVERT: C 646 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.5463 (ppp80) REVERT: C 650 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8395 (mp) REVERT: C 782 ARG cc_start: 0.8195 (mtp85) cc_final: 0.6698 (ptt90) REVERT: C 807 ASP cc_start: 0.6948 (m-30) cc_final: 0.6679 (m-30) REVERT: C 827 ARG cc_start: 0.6955 (mmm-85) cc_final: 0.6493 (mmm160) REVERT: E 511 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7754 (p90) REVERT: E 589 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7617 (ttt90) REVERT: E 593 ASN cc_start: 0.8242 (m110) cc_final: 0.8038 (m110) REVERT: E 621 ASP cc_start: 0.9146 (t70) cc_final: 0.8945 (t0) REVERT: E 646 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.4888 (ppp80) REVERT: E 650 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7264 (mp) REVERT: E 658 GLU cc_start: 0.7331 (tp30) cc_final: 0.6519 (mp0) REVERT: E 663 MET cc_start: 0.5187 (tpt) cc_final: 0.3418 (tpt) REVERT: E 676 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8013 (mp) REVERT: E 782 ARG cc_start: 0.8486 (mtp85) cc_final: 0.7627 (mpt180) outliers start: 24 outliers final: 14 residues processed: 183 average time/residue: 0.0977 time to fit residues: 24.0131 Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.154870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130740 restraints weight = 10494.640| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.48 r_work: 0.3267 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9162 Z= 0.102 Angle : 0.466 5.145 12474 Z= 0.232 Chirality : 0.040 0.147 1504 Planarity : 0.005 0.050 1494 Dihedral : 6.667 57.776 1250 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.42 % Allowed : 13.58 % Favored : 84.00 % 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: 2.37 (0.25), residues: 1102 helix: 2.22 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.19 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 388 TYR 0.013 0.001 TYR C 519 PHE 0.014 0.001 PHE C 471 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 9158) covalent geometry : angle 0.46576 / 0.23 (12462) hydrogen bonds : bond 0.03431 / 2.37 ( 576) hydrogen bonds : angle 3.96321 / 2.92 ( 1662) link_BETA1-4 : bond 0.00243 / 0.14 ( 2) link_BETA1-4 : angle 0.95838 / 0.49 ( 6) link_NAG-ASN : bond 0.00131 / 0.08 ( 2) link_NAG-ASN : angle 0.86428 / 0.47 ( 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 191 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.332 Fit side-chains REVERT: B 83 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7019 (tt) REVERT: C 499 LEU cc_start: 0.7677 (tp) cc_final: 0.7262 (tt) REVERT: C 559 MET cc_start: 0.6190 (mmm) cc_final: 0.5207 (ttp) REVERT: C 646 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.5455 (ppp80) REVERT: C 650 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 782 ARG cc_start: 0.8196 (mtp85) cc_final: 0.6691 (ptt90) REVERT: C 807 ASP cc_start: 0.6937 (m-30) cc_final: 0.6666 (m-30) REVERT: C 827 ARG cc_start: 0.6986 (mmm-85) cc_final: 0.6490 (mmm160) REVERT: E 480 GLU cc_start: 0.7053 (tt0) cc_final: 0.6833 (tt0) REVERT: E 589 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7628 (ttt90) REVERT: E 621 ASP cc_start: 0.9150 (t70) cc_final: 0.8928 (t0) REVERT: E 646 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5092 (ppp80) REVERT: E 650 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7296 (mp) REVERT: E 658 GLU cc_start: 0.7320 (tp30) cc_final: 0.6502 (mp0) REVERT: E 663 MET cc_start: 0.5175 (tpt) cc_final: 0.3412 (tpt) REVERT: E 676 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8026 (mp) REVERT: E 782 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7660 (mpt180) outliers start: 23 outliers final: 14 residues processed: 183 average time/residue: 0.1064 time to fit residues: 26.3663 Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.154312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130460 restraints weight = 10555.943| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.46 r_work: 0.3265 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9162 Z= 0.108 Angle : 0.471 5.176 12474 Z= 0.234 Chirality : 0.040 0.153 1504 Planarity : 0.005 0.050 1494 Dihedral : 6.661 57.837 1250 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.53 % Allowed : 13.58 % Favored : 83.89 % 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: 2.37 (0.26), residues: 1102 helix: 2.21 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.20 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 384 TYR 0.013 0.001 TYR C 519 PHE 0.014 0.001 PHE C 471 TRP 0.012 0.001 TRP C 492 HIS 0.002 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9158) covalent geometry : angle 0.46998 / 0.23 (12462) hydrogen bonds : bond 0.03480 / 2.40 ( 576) hydrogen bonds : angle 3.98717 / 2.95 ( 1662) link_BETA1-4 : bond 0.00245 / 0.14 ( 2) link_BETA1-4 : angle 0.96008 / 0.49 ( 6) link_NAG-ASN : bond 0.00143 / 0.08 ( 2) link_NAG-ASN : angle 0.85233 / 0.47 ( 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 190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.303 Fit side-chains REVERT: B 83 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7029 (tt) REVERT: C 384 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.6425 (ttp-110) REVERT: C 430 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8100 (ttmt) REVERT: C 499 LEU cc_start: 0.7667 (tp) cc_final: 0.7257 (tt) REVERT: C 559 MET cc_start: 0.6196 (mmm) cc_final: 0.5219 (ttp) REVERT: C 646 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.5478 (ppp80) REVERT: C 650 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8392 (mp) REVERT: C 693 GLU cc_start: 0.8572 (pm20) cc_final: 0.8299 (pm20) REVERT: C 782 ARG cc_start: 0.8191 (mtp85) cc_final: 0.6695 (ptt90) REVERT: C 807 ASP cc_start: 0.6910 (m-30) cc_final: 0.6635 (m-30) REVERT: C 827 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6475 (mmm160) REVERT: E 457 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: E 480 GLU cc_start: 0.7037 (tt0) cc_final: 0.6816 (tt0) REVERT: E 511 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7798 (p90) REVERT: E 589 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7642 (ttt90) REVERT: E 646 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.5089 (ppp80) REVERT: E 650 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7338 (mp) REVERT: E 658 GLU cc_start: 0.7311 (tp30) cc_final: 0.6487 (mp0) REVERT: E 663 MET cc_start: 0.5175 (tpt) cc_final: 0.3406 (tpt) REVERT: E 676 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8024 (mp) REVERT: E 782 ARG cc_start: 0.8500 (mtp85) cc_final: 0.7648 (mpt180) outliers start: 24 outliers final: 15 residues processed: 181 average time/residue: 0.1069 time to fit residues: 26.1091 Evaluate side-chains 187 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 457 GLN Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain E residue 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 877 ILE Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.155250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.131306 restraints weight = 10423.881| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.47 r_work: 0.3272 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9162 Z= 0.103 Angle : 0.469 5.152 12474 Z= 0.233 Chirality : 0.040 0.134 1504 Planarity : 0.005 0.050 1494 Dihedral : 6.626 58.268 1250 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.63 % Allowed : 13.58 % Favored : 83.79 % 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: 2.47 (0.25), residues: 1102 helix: 2.31 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.27 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 384 TYR 0.013 0.001 TYR C 519 PHE 0.014 0.001 PHE C 471 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9158) covalent geometry : angle 0.46861 / 0.23 (12462) hydrogen bonds : bond 0.03414 / 2.36 ( 576) hydrogen bonds : angle 3.96643 / 2.93 ( 1662) link_BETA1-4 : bond 0.00237 / 0.14 ( 2) link_BETA1-4 : angle 0.96407 / 0.49 ( 6) link_NAG-ASN : bond 0.00155 / 0.09 ( 2) link_NAG-ASN : angle 0.83453 / 0.46 ( 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 193 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.289 Fit side-chains REVERT: B 83 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7029 (tt) REVERT: C 384 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.6404 (ttp-110) REVERT: C 499 LEU cc_start: 0.7661 (tp) cc_final: 0.7232 (tt) REVERT: C 559 MET cc_start: 0.6216 (mmm) cc_final: 0.5266 (ttp) REVERT: C 646 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.5465 (ppp80) REVERT: C 650 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8393 (mp) REVERT: C 693 GLU cc_start: 0.8573 (pm20) cc_final: 0.8305 (pm20) REVERT: C 782 ARG cc_start: 0.8180 (mtp85) cc_final: 0.6682 (ptt90) REVERT: C 807 ASP cc_start: 0.6907 (m-30) cc_final: 0.6631 (m-30) REVERT: C 827 ARG cc_start: 0.6965 (mmm-85) cc_final: 0.6502 (mmm160) REVERT: E 480 GLU cc_start: 0.7037 (tt0) cc_final: 0.6812 (tt0) REVERT: E 511 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7800 (p90) REVERT: E 589 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7644 (ttt90) REVERT: E 646 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.5188 (ppp80) REVERT: E 650 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7291 (mp) REVERT: E 658 GLU cc_start: 0.7312 (tp30) cc_final: 0.6487 (mp0) REVERT: E 663 MET cc_start: 0.5167 (tpt) cc_final: 0.3405 (tpt) REVERT: E 782 ARG cc_start: 0.8517 (mtp85) cc_final: 0.7675 (mpt180) outliers start: 25 outliers final: 16 residues processed: 184 average time/residue: 0.1094 time to fit residues: 27.0751 Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 629 THR 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 776 MET Chi-restraints excluded: chain E residue 822 VAL Chi-restraints excluded: chain E residue 877 ILE Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 77 optimal weight: 0.0060 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.156858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.132929 restraints weight = 10332.316| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.47 r_work: 0.3294 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 9162 Z= 0.096 Angle : 0.461 5.095 12474 Z= 0.233 Chirality : 0.039 0.140 1504 Planarity : 0.004 0.049 1494 Dihedral : 6.512 59.119 1250 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.32 % Allowed : 13.89 % Favored : 83.79 % 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: 2.44 (0.25), residues: 1102 helix: 2.30 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.20 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 384 TYR 0.011 0.001 TYR C 519 PHE 0.014 0.001 PHE C 471 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 9158) covalent geometry : angle 0.46064 / 0.23 (12462) hydrogen bonds : bond 0.03260 / 2.26 ( 576) hydrogen bonds : angle 3.95697 / 2.90 ( 1662) link_BETA1-4 : bond 0.00260 / 0.15 ( 2) link_BETA1-4 : angle 0.96703 / 0.50 ( 6) link_NAG-ASN : bond 0.00171 / 0.10 ( 2) link_NAG-ASN : angle 0.77495 / 0.43 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.97 seconds wall clock time: 46 minutes 22.65 seconds (2782.65 seconds total)