Starting phenix.real_space_refine on Thu Jul 2 14:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ct3_26979/07_2026/8ct3_26979.cif" } 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= 0.122 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 6006 2.51 5 N 1406 2.21 5 O 1508 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: 8964 Number of models: 1 Model: "" Number of chains: 6 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: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.64, per 1000 atoms: 0.18 Number of scatterers: 8964 At special positions: 0 Unit cell: (145.665, 79.68, 105.41, 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 1508 8.00 N 1406 7.00 C 6006 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 NAG-ASN " NAG C1002 " - " ASN C 642 " " NAG E1002 " - " ASN E 642 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 224.3 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 75.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 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: 3.641A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.653A 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: 3.541A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.551A 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: 3.801A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.524A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.728A 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: 3.550A pdb=" N LEU C 869 " --> pdb=" O LEU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.836A pdb=" N LEU C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) 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: 3.640A pdb=" N LEU E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.596A 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 483 Processing helix chain 'E' and resid 485 through 507 removed outlier: 3.653A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 516 Processing helix chain 'E' and resid 517 through 547 removed outlier: 3.542A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 594 removed outlier: 3.552A 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: 3.801A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.525A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.727A 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 removed outlier: 3.551A pdb=" N LEU E 869 " --> pdb=" O LEU E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 878 removed outlier: 3.837A pdb=" N LEU E 876 " --> pdb=" O VAL E 872 " (cutoff:3.500A) removed outlier: 3.804A 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 742 removed outlier: 6.946A pdb=" N VAL C 740 " --> pdb=" O GLN C 754 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN C 752 " --> pdb=" O GLY C 742 " (cutoff:3.500A) 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 742 removed outlier: 6.946A pdb=" N VAL E 740 " --> pdb=" O GLN E 754 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN E 752 " --> pdb=" O GLY E 742 " (cutoff:3.500A) 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: 0.96 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1308 1.31 - 1.43: 2420 1.43 - 1.56: 5386 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9192 Sorted by residual: bond pdb=" C1B PIO C1004 " pdb=" O3C PIO C1004 " 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 E1004 " pdb=" O3C PIO E1004 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1A PIO C1004 " pdb=" O2C PIO C1004 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C1A PIO E1004 " pdb=" O2C PIO E1004 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O4 PIO C1004 " pdb=" P4 PIO C1004 " ideal model delta sigma weight residual 1.710 1.647 0.063 2.00e-02 2.50e+03 9.87e+00 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12370 2.45 - 4.89: 107 4.89 - 7.34: 33 7.34 - 9.79: 6 9.79 - 12.23: 4 Bond angle restraints: 12520 Sorted by residual: angle pdb=" O1 PIO C1004 " pdb=" P1 PIO C1004 " pdb=" O13 PIO C1004 " ideal model delta sigma weight residual 97.64 109.87 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O1 PIO E1004 " pdb=" P1 PIO E1004 " pdb=" O13 PIO E1004 " ideal model delta sigma weight residual 97.64 109.86 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O11 PIO C1004 " pdb=" P1 PIO C1004 " pdb=" O12 PIO C1004 " ideal model delta sigma weight residual 121.09 109.44 11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O11 PIO E1004 " pdb=" P1 PIO E1004 " pdb=" O12 PIO E1004 " ideal model delta sigma weight residual 121.09 109.47 11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C2A PIO E1004 " pdb=" C1A PIO E1004 " pdb=" O2C PIO E1004 " ideal model delta sigma weight residual 110.66 119.78 -9.12 3.00e+00 1.11e-01 9.24e+00 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5098 17.60 - 35.20: 174 35.20 - 52.80: 48 52.80 - 70.40: 6 70.40 - 88.00: 6 Dihedral angle restraints: 5332 sinusoidal: 2130 harmonic: 3202 Sorted by residual: dihedral pdb=" CB MET E 587 " pdb=" CG MET E 587 " pdb=" SD MET E 587 " pdb=" CE MET E 587 " ideal model delta sinusoidal sigma weight residual 60.00 108.67 -48.67 3 1.50e+01 4.44e-03 8.67e+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 60.00 108.63 -48.63 3 1.50e+01 4.44e-03 8.67e+00 dihedral pdb=" N GLU C 473 " pdb=" CA GLU C 473 " pdb=" CB GLU C 473 " pdb=" CG GLU C 473 " ideal model delta sinusoidal sigma weight residual -60.00 -108.31 48.31 3 1.50e+01 4.44e-03 8.62e+00 ... (remaining 5329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 875 0.024 - 0.048: 312 0.048 - 0.072: 210 0.072 - 0.096: 56 0.096 - 0.119: 57 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA ILE C 783 " pdb=" N ILE C 783 " pdb=" C ILE C 783 " pdb=" CB ILE C 783 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL C 828 " pdb=" N VAL C 828 " pdb=" C VAL C 828 " pdb=" CB VAL C 828 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1507 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO C 391 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO E 391 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.033 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 4.40e-02 3.10e+00 pdb=" N PRO C 467 " 0.076 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 1491 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 969 2.75 - 3.29: 9083 3.29 - 3.83: 15260 3.83 - 4.36: 17742 4.36 - 4.90: 30938 Nonbonded interactions: 73992 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.216 3.040 nonbonded pdb=" O LEU C 427 " pdb=" OG1 THR C 431 " model vdw 2.271 3.040 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR E 375 " pdb=" OE2 GLU E 508 " model vdw 2.279 3.040 ... (remaining 73987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.560 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 9194 Z= 0.164 Angle : 0.643 12.233 12526 Z= 0.299 Chirality : 0.039 0.119 1510 Planarity : 0.005 0.058 1492 Dihedral : 10.553 87.999 3268 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.63 % Allowed : 3.37 % Favored : 96.00 % 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: 1.87 (0.25), residues: 1102 helix: 1.71 (0.18), residues: 766 sheet: None (None), residues: 0 loop : 0.28 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 389 TYR 0.010 0.001 TYR E 519 PHE 0.008 0.001 PHE C 471 TRP 0.006 0.001 TRP C 831 HIS 0.002 0.000 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 9192) covalent geometry : angle 0.64342 / 0.30 (12520) hydrogen bonds : bond 0.15704 / 10.48 ( 576) hydrogen bonds : angle 4.99253 / 3.69 ( 1662) link_NAG-ASN : bond 0.00174 / 0.10 ( 2) link_NAG-ASN : angle 0.60428 / 0.34 ( 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 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: D 100 MET cc_start: 0.4256 (ttm) cc_final: 0.3126 (tmm) REVERT: C 533 ILE cc_start: 0.7454 (mt) cc_final: 0.7233 (mt) REVERT: C 551 LYS cc_start: 0.5378 (tttt) cc_final: 0.4853 (mttt) REVERT: C 639 LYS cc_start: 0.5814 (pttp) cc_final: 0.5580 (pttt) REVERT: E 646 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.4799 (ppp80) outliers start: 6 outliers final: 3 residues processed: 154 average time/residue: 0.0790 time to fit residues: 16.8215 Evaluate side-chains 122 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 646 ARG 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: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 377 GLN C 630 GLN C 651 HIS C 683 GLN E 377 GLN E 630 GLN E 683 GLN E 819 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.171269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147872 restraints weight = 10109.526| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.38 r_work: 0.3480 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9194 Z= 0.210 Angle : 0.629 6.430 12526 Z= 0.312 Chirality : 0.045 0.151 1510 Planarity : 0.005 0.047 1492 Dihedral : 8.057 69.178 1269 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.42 % Allowed : 6.11 % Favored : 91.47 % 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: 1.51 (0.25), residues: 1102 helix: 1.43 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.19 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 389 TYR 0.028 0.003 TYR E 519 PHE 0.019 0.002 PHE C 836 TRP 0.020 0.002 TRP E 492 HIS 0.008 0.002 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 ( 9192) covalent geometry : angle 0.62866 / 0.31 (12520) hydrogen bonds : bond 0.04995 / 3.44 ( 576) hydrogen bonds : angle 4.36648 / 3.20 ( 1662) link_NAG-ASN : bond 0.00262 / 0.15 ( 2) link_NAG-ASN : angle 1.43653 / 0.74 ( 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 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5694 (tttt) cc_final: 0.5019 (mttt) REVERT: C 782 ARG cc_start: 0.7220 (mtp85) cc_final: 0.6692 (mtp180) REVERT: E 646 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.4685 (ppp80) REVERT: E 700 SER cc_start: 0.8127 (p) cc_final: 0.7715 (m) REVERT: E 839 ILE cc_start: 0.7374 (tp) cc_final: 0.7089 (mt) outliers start: 23 outliers final: 17 residues processed: 159 average time/residue: 0.0699 time to fit residues: 16.0316 Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 457 GLN E 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.148382 restraints weight = 9950.928| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.30 r_work: 0.3484 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9194 Z= 0.143 Angle : 0.521 6.965 12526 Z= 0.258 Chirality : 0.041 0.200 1510 Planarity : 0.005 0.044 1492 Dihedral : 7.786 70.439 1268 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.16 % Allowed : 8.11 % Favored : 88.74 % 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: 1.64 (0.25), residues: 1102 helix: 1.68 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.09 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 387 TYR 0.019 0.002 TYR E 519 PHE 0.020 0.002 PHE C 476 TRP 0.012 0.001 TRP E 492 HIS 0.004 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9192) covalent geometry : angle 0.52016 / 0.26 (12520) hydrogen bonds : bond 0.04269 / 2.93 ( 576) hydrogen bonds : angle 4.19475 / 3.08 ( 1662) link_NAG-ASN : bond 0.00158 / 0.09 ( 2) link_NAG-ASN : angle 1.04092 / 0.53 ( 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: 30 poor density : 141 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5758 (tttt) cc_final: 0.5071 (mttt) REVERT: C 639 LYS cc_start: 0.6138 (pttp) cc_final: 0.5862 (pttt) REVERT: C 782 ARG cc_start: 0.7299 (mtp85) cc_final: 0.6752 (mtp180) REVERT: E 426 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6537 (mp) REVERT: E 646 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.4710 (ppp80) REVERT: E 839 ILE cc_start: 0.7370 (tp) cc_final: 0.7094 (mt) outliers start: 30 outliers final: 24 residues processed: 160 average time/residue: 0.0787 time to fit residues: 17.9097 Evaluate side-chains 156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 639 LYS Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN E 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.171285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.147307 restraints weight = 10067.196| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.37 r_work: 0.3485 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9194 Z= 0.115 Angle : 0.483 5.290 12526 Z= 0.239 Chirality : 0.040 0.141 1510 Planarity : 0.004 0.042 1492 Dihedral : 7.552 69.813 1268 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.63 % Allowed : 9.89 % Favored : 87.47 % 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: 1.83 (0.25), residues: 1102 helix: 1.79 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -0.00 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 808 TYR 0.015 0.002 TYR E 519 PHE 0.018 0.001 PHE C 476 TRP 0.010 0.001 TRP E 492 HIS 0.003 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 9192) covalent geometry : angle 0.48249 / 0.24 (12520) hydrogen bonds : bond 0.03853 / 2.65 ( 576) hydrogen bonds : angle 4.08989 / 3.01 ( 1662) link_NAG-ASN : bond 0.00107 / 0.06 ( 2) link_NAG-ASN : angle 0.94115 / 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 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5769 (tttt) cc_final: 0.5043 (mttt) REVERT: C 553 TYR cc_start: 0.7580 (m-80) cc_final: 0.7045 (m-80) REVERT: C 782 ARG cc_start: 0.7282 (mtp85) cc_final: 0.6692 (mtp180) REVERT: C 817 LYS cc_start: 0.8261 (pttt) cc_final: 0.7967 (pptt) REVERT: E 426 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6567 (mp) REVERT: E 646 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.4665 (ppp80) REVERT: E 839 ILE cc_start: 0.7327 (tp) cc_final: 0.7068 (mt) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.0842 time to fit residues: 17.9896 Evaluate side-chains 154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 57 optimal weight: 0.3980 chunk 58 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.0060 chunk 43 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 chunk 91 optimal weight: 0.0020 overall best weight: 0.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 457 GLN E 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.175230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.153215 restraints weight = 9974.779| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.24 r_work: 0.3547 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9194 Z= 0.091 Angle : 0.455 10.013 12526 Z= 0.222 Chirality : 0.039 0.130 1510 Planarity : 0.004 0.040 1492 Dihedral : 7.231 68.805 1266 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.63 % Allowed : 10.21 % 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: 2.20 (0.25), residues: 1102 helix: 2.06 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.16 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 760 TYR 0.014 0.001 TYR C 486 PHE 0.021 0.001 PHE C 476 TRP 0.008 0.001 TRP E 831 HIS 0.002 0.000 HIS E 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 ( 9192) covalent geometry : angle 0.45535 / 0.22 (12520) hydrogen bonds : bond 0.03360 / 2.31 ( 576) hydrogen bonds : angle 3.91751 / 2.89 ( 1662) link_NAG-ASN : bond 0.00172 / 0.10 ( 2) link_NAG-ASN : angle 0.69157 / 0.36 ( 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 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: D 100 MET cc_start: 0.5367 (ttm) cc_final: 0.2991 (tmm) REVERT: C 551 LYS cc_start: 0.5663 (tttt) cc_final: 0.5026 (mttt) REVERT: C 553 TYR cc_start: 0.7559 (m-80) cc_final: 0.7055 (m-80) REVERT: C 782 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6625 (mtp180) REVERT: C 817 LYS cc_start: 0.8176 (pttt) cc_final: 0.7831 (pttt) REVERT: E 426 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6474 (mp) REVERT: E 646 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.4646 (ppp80) REVERT: E 650 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5248 (mp) REVERT: E 839 ILE cc_start: 0.7274 (tp) cc_final: 0.6967 (mt) outliers start: 25 outliers final: 20 residues processed: 149 average time/residue: 0.0743 time to fit residues: 16.0891 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 639 LYS Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.169259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.145110 restraints weight = 10025.893| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.38 r_work: 0.3460 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9194 Z= 0.142 Angle : 0.537 9.180 12526 Z= 0.260 Chirality : 0.042 0.175 1510 Planarity : 0.004 0.039 1492 Dihedral : 7.334 69.869 1266 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.05 % Allowed : 11.05 % 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: 1.87 (0.25), residues: 1102 helix: 1.85 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.00 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 589 TYR 0.020 0.002 TYR E 519 PHE 0.015 0.002 PHE E 471 TRP 0.011 0.001 TRP E 492 HIS 0.003 0.001 HIS E 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9192) covalent geometry : angle 0.53641 / 0.26 (12520) hydrogen bonds : bond 0.04031 / 2.79 ( 576) hydrogen bonds : angle 4.10576 / 3.04 ( 1662) link_NAG-ASN : bond 0.00101 / 0.06 ( 2) link_NAG-ASN : angle 1.04353 / 0.53 ( 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 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5788 (tttt) cc_final: 0.5161 (mttt) REVERT: C 639 LYS cc_start: 0.6158 (pttp) cc_final: 0.5889 (pttt) REVERT: C 782 ARG cc_start: 0.7304 (mtp85) cc_final: 0.6746 (mtp180) REVERT: E 426 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6610 (mp) REVERT: E 441 LEU cc_start: 0.7609 (mp) cc_final: 0.7379 (mp) REVERT: E 646 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.4696 (ppp80) REVERT: E 700 SER cc_start: 0.8089 (p) cc_final: 0.7783 (m) REVERT: E 839 ILE cc_start: 0.7350 (tp) cc_final: 0.7098 (mt) outliers start: 29 outliers final: 24 residues processed: 154 average time/residue: 0.0788 time to fit residues: 16.9161 Evaluate side-chains 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Chi-restraints excluded: chain E residue 883 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 819 HIS E 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.165486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141685 restraints weight = 10052.170| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.34 r_work: 0.3421 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9194 Z= 0.169 Angle : 0.584 8.563 12526 Z= 0.285 Chirality : 0.043 0.194 1510 Planarity : 0.005 0.039 1492 Dihedral : 7.538 71.771 1266 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.37 % Allowed : 11.47 % 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: 1.26 (0.25), residues: 1102 helix: 1.46 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 589 TYR 0.023 0.002 TYR E 519 PHE 0.023 0.002 PHE C 476 TRP 0.013 0.002 TRP C 492 HIS 0.004 0.001 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 9192) covalent geometry : angle 0.58350 / 0.29 (12520) hydrogen bonds : bond 0.04479 / 3.09 ( 576) hydrogen bonds : angle 4.29665 / 3.18 ( 1662) link_NAG-ASN : bond 0.00064 / 0.04 ( 2) link_NAG-ASN : angle 1.38095 / 0.70 ( 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 171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.208 Fit side-chains REVERT: C 639 LYS cc_start: 0.6265 (pttp) cc_final: 0.6045 (pttt) REVERT: C 782 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6832 (mtp180) REVERT: C 817 LYS cc_start: 0.8463 (pttt) cc_final: 0.8171 (pttt) REVERT: E 426 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6650 (mp) REVERT: E 646 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.4875 (ppp80) REVERT: E 700 SER cc_start: 0.8134 (p) cc_final: 0.7819 (m) REVERT: E 839 ILE cc_start: 0.7395 (tp) cc_final: 0.7136 (mt) outliers start: 32 outliers final: 28 residues processed: 159 average time/residue: 0.0709 time to fit residues: 16.0918 Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.169306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147510 restraints weight = 9941.644| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.27 r_work: 0.3475 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 9194 Z= 0.113 Angle : 0.504 8.054 12526 Z= 0.248 Chirality : 0.040 0.141 1510 Planarity : 0.004 0.040 1492 Dihedral : 7.218 69.592 1266 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.76 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: 1.70 (0.25), residues: 1102 helix: 1.79 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.26 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 760 TYR 0.013 0.001 TYR E 519 PHE 0.022 0.001 PHE C 476 TRP 0.008 0.001 TRP E 831 HIS 0.002 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9192) covalent geometry : angle 0.50406 / 0.25 (12520) hydrogen bonds : bond 0.03814 / 2.64 ( 576) hydrogen bonds : angle 4.13831 / 3.07 ( 1662) link_NAG-ASN : bond 0.00124 / 0.08 ( 2) link_NAG-ASN : angle 0.98561 / 0.50 ( 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 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.326 Fit side-chains REVERT: C 639 LYS cc_start: 0.6260 (pttp) cc_final: 0.6053 (pttt) REVERT: C 782 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6793 (mtp180) REVERT: C 817 LYS cc_start: 0.8431 (pttt) cc_final: 0.8083 (pttt) REVERT: E 426 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6583 (mp) REVERT: E 646 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.4848 (ppp80) REVERT: E 700 SER cc_start: 0.8054 (p) cc_final: 0.7734 (m) REVERT: E 839 ILE cc_start: 0.7337 (tp) cc_final: 0.7023 (mt) outliers start: 28 outliers final: 24 residues processed: 157 average time/residue: 0.0848 time to fit residues: 18.7222 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 0.0050 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.168067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146122 restraints weight = 9937.427| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.32 r_work: 0.3459 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9194 Z= 0.127 Angle : 0.532 12.126 12526 Z= 0.258 Chirality : 0.041 0.187 1510 Planarity : 0.004 0.040 1492 Dihedral : 7.190 69.419 1266 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.05 % Allowed : 12.42 % 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: 1.68 (0.25), residues: 1102 helix: 1.76 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.22 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 760 TYR 0.016 0.002 TYR E 519 PHE 0.015 0.001 PHE E 471 TRP 0.010 0.001 TRP C 492 HIS 0.003 0.001 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9192) covalent geometry : angle 0.53140 / 0.26 (12520) hydrogen bonds : bond 0.03922 / 2.72 ( 576) hydrogen bonds : angle 4.15454 / 3.09 ( 1662) link_NAG-ASN : bond 0.00071 / 0.04 ( 2) link_NAG-ASN : angle 1.02176 / 0.52 ( 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 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.396 Fit side-chains REVERT: C 782 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6787 (mtp180) REVERT: C 817 LYS cc_start: 0.8471 (pttt) cc_final: 0.8118 (pttt) REVERT: E 426 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6591 (mp) REVERT: E 646 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.4873 (ppp80) REVERT: E 839 ILE cc_start: 0.7343 (tp) cc_final: 0.7088 (mt) outliers start: 29 outliers final: 24 residues processed: 152 average time/residue: 0.0937 time to fit residues: 19.8907 Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 761 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 82 optimal weight: 0.0570 chunk 94 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 overall best weight: 0.7312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 457 GLN E 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.169782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145986 restraints weight = 10002.947| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.37 r_work: 0.3473 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9194 Z= 0.112 Angle : 0.519 11.239 12526 Z= 0.251 Chirality : 0.040 0.186 1510 Planarity : 0.004 0.040 1492 Dihedral : 7.021 68.559 1262 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 1.80 (0.25), residues: 1102 helix: 1.87 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.21 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 760 TYR 0.014 0.001 TYR C 486 PHE 0.029 0.001 PHE C 476 TRP 0.010 0.001 TRP C 492 HIS 0.002 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9192) covalent geometry : angle 0.51907 / 0.25 (12520) hydrogen bonds : bond 0.03740 / 2.58 ( 576) hydrogen bonds : angle 4.10877 / 3.06 ( 1662) link_NAG-ASN : bond 0.00102 / 0.06 ( 2) link_NAG-ASN : angle 0.91162 / 0.47 ( 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 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.345 Fit side-chains REVERT: C 553 TYR cc_start: 0.7679 (m-80) cc_final: 0.7335 (m-80) REVERT: C 782 ARG cc_start: 0.7369 (mtp85) cc_final: 0.6828 (mtp180) REVERT: C 817 LYS cc_start: 0.8428 (pttt) cc_final: 0.8072 (pttt) REVERT: E 426 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6703 (mp) REVERT: E 441 LEU cc_start: 0.7652 (mp) cc_final: 0.7448 (mp) REVERT: E 646 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.4911 (ppp80) REVERT: E 700 SER cc_start: 0.8339 (p) cc_final: 0.8010 (m) REVERT: E 839 ILE cc_start: 0.7328 (tp) cc_final: 0.7008 (mt) outliers start: 25 outliers final: 22 residues processed: 149 average time/residue: 0.0888 time to fit residues: 18.6009 Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 639 LYS Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.170021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148218 restraints weight = 9841.303| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.26 r_work: 0.3485 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9194 Z= 0.110 Angle : 0.514 11.444 12526 Z= 0.249 Chirality : 0.040 0.171 1510 Planarity : 0.004 0.038 1492 Dihedral : 6.941 68.017 1262 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.95 % Allowed : 12.84 % Favored : 84.21 % 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: 1.86 (0.25), residues: 1102 helix: 1.91 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.18 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 389 TYR 0.013 0.001 TYR E 519 PHE 0.030 0.001 PHE C 476 TRP 0.009 0.001 TRP E 831 HIS 0.005 0.001 HIS C 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9192) covalent geometry : angle 0.51384 / 0.25 (12520) hydrogen bonds : bond 0.03700 / 2.56 ( 576) hydrogen bonds : angle 4.08001 / 3.04 ( 1662) link_NAG-ASN : bond 0.00100 / 0.06 ( 2) link_NAG-ASN : angle 0.89237 / 0.47 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.42 seconds wall clock time: 41 minutes 36.33 seconds (2496.33 seconds total)