Starting phenix.real_space_refine on Thu Jul 2 17:30:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v07_26940/07_2026/7v07_26940.cif" } resolution = 2.8 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= 0.001 sd= 0.162 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 8 5.49 5 S 38 5.16 5 C 6134 2.51 5 N 1410 2.21 5 O 1572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 9162 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 192 Unusual residues: {'CLR': 2, 'PIO': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.71, per 1000 atoms: 0.19 Number of scatterers: 9162 At special positions: 0 Unit cell: (142.345, 86.735, 115.785, 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 8 15.00 O 1572 8.00 N 1410 7.00 C 6134 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 ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-4 " BMA A 3 " - " MAN A 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG A 1 " - " FUC A 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 6 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 322.4 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: 59 helices and 4 sheets defined 74.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 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 removed outlier: 3.536A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) 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: 3.636A 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 482 Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.626A 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 Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.638A 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: 3.650A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 703 through 719 removed outlier: 3.751A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.701A 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 773 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 813 removed outlier: 4.069A pdb=" N PHE C 813 " --> pdb=" O ILE C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 829 through 853 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 Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.794A pdb=" N LEU C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 3.746A 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 432 removed outlier: 3.632A pdb=" N LEU E 406 " --> pdb=" O SER E 402 " (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: 3.541A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.560A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 547 removed outlier: 3.642A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 593 removed outlier: 3.533A 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 624 Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.740A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.825A 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 703 through 719 removed outlier: 3.752A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.722A 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 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: 3.682A pdb=" N LEU E 788 " --> pdb=" O PRO E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 813 removed outlier: 4.041A pdb=" N PHE E 813 " --> pdb=" O ILE E 809 " (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: 3.500A pdb=" N LEU E 869 " --> pdb=" O LEU E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 878 removed outlier: 3.858A 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 741 575 hydrogen bonds defined for protein. 1674 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: 1.13 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1318 1.32 - 1.44: 2473 1.44 - 1.56: 5510 1.56 - 1.69: 17 1.69 - 1.81: 70 Bond restraints: 9388 Sorted by residual: bond pdb=" C PRO E 815 " pdb=" O PRO E 815 " ideal model delta sigma weight residual 1.246 1.195 0.051 8.50e-03 1.38e+04 3.54e+01 bond pdb=" C PRO C 815 " pdb=" O PRO C 815 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.38e+01 bond pdb=" O4 PIO E1005 " pdb=" P4 PIO E1005 " ideal model delta sigma weight residual 1.710 1.600 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" O4 PIO E1004 " pdb=" P4 PIO E1004 " ideal model delta sigma weight residual 1.710 1.601 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" O5 PIO E1005 " pdb=" P5 PIO E1005 " ideal model delta sigma weight residual 1.699 1.600 0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 9383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 12066 2.09 - 4.18: 614 4.18 - 6.28: 80 6.28 - 8.37: 9 8.37 - 10.46: 5 Bond angle restraints: 12774 Sorted by residual: angle pdb=" C ARG D 80 " pdb=" CA ARG D 80 " pdb=" CB ARG D 80 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" C TYR C 818 " pdb=" CA TYR C 818 " pdb=" CB TYR C 818 " ideal model delta sigma weight residual 110.79 119.42 -8.63 1.66e+00 3.63e-01 2.70e+01 angle pdb=" N PRO C 598 " pdb=" CA PRO C 598 " pdb=" C PRO C 598 " ideal model delta sigma weight residual 111.14 103.04 8.10 1.56e+00 4.11e-01 2.69e+01 angle pdb=" N GLN E 434 " pdb=" CA GLN E 434 " pdb=" C GLN E 434 " ideal model delta sigma weight residual 111.28 105.84 5.44 1.09e+00 8.42e-01 2.49e+01 angle pdb=" N PRO C 568 " pdb=" CA PRO C 568 " pdb=" C PRO C 568 " ideal model delta sigma weight residual 111.21 118.32 -7.11 1.59e+00 3.96e-01 2.00e+01 ... (remaining 12769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4575 17.72 - 35.43: 557 35.43 - 53.15: 181 53.15 - 70.87: 45 70.87 - 88.58: 20 Dihedral angle restraints: 5378 sinusoidal: 2176 harmonic: 3202 Sorted by residual: dihedral pdb=" C TYR C 818 " pdb=" N TYR C 818 " pdb=" CA TYR C 818 " pdb=" CB TYR C 818 " ideal model delta harmonic sigma weight residual -122.60 -132.98 10.38 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C ASN C 433 " pdb=" N ASN C 433 " pdb=" CA ASN C 433 " pdb=" CB ASN C 433 " ideal model delta harmonic sigma weight residual -122.60 -132.28 9.68 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C ASN E 433 " pdb=" N ASN E 433 " pdb=" CA ASN E 433 " pdb=" CB ASN E 433 " ideal model delta harmonic sigma weight residual -122.60 -132.17 9.57 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1323 0.074 - 0.147: 188 0.147 - 0.221: 38 0.221 - 0.294: 10 0.294 - 0.368: 3 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C1 MAN A 5 " pdb=" O4 BMA A 3 " pdb=" C2 MAN A 5 " pdb=" O5 MAN A 5 " both_signs ideal model delta sigma weight residual False 2.40 2.03 0.37 2.00e-02 2.50e+03 3.39e+02 chirality pdb=" C1 MAN F 5 " pdb=" O4 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.32e+02 chirality pdb=" CA LYS C 817 " pdb=" N LYS C 817 " pdb=" C LYS C 817 " pdb=" CB LYS C 817 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1559 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 874 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO E 875 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E 875 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 875 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 470 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C VAL C 470 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL C 470 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 471 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 429 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C GLU E 429 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU E 429 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS E 430 " 0.019 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1933 2.78 - 3.31: 8850 3.31 - 3.84: 15960 3.84 - 4.37: 18935 4.37 - 4.90: 31478 Nonbonded interactions: 77156 Sorted by model distance: nonbonded pdb=" OG1 THR C 375 " pdb=" OE2 GLU C 508 " model vdw 2.251 3.040 nonbonded pdb=" OG SER C 529 " pdb=" OG SER C 799 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP C 636 " pdb=" NZ LYS C 639 " model vdw 2.296 3.120 nonbonded pdb=" O SER C 644 " pdb=" NH2 ARG C 656 " model vdw 2.313 3.120 nonbonded pdb=" OG SER C 438 " pdb=" OE2 GLU C 439 " model vdw 2.322 3.040 ... (remaining 77151 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' and resid 371 through 1003) } 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.590 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.020 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.007 0.110 9400 Z= 0.438 Angle : 0.973 11.322 12810 Z= 0.613 Chirality : 0.059 0.368 1562 Planarity : 0.007 0.093 1498 Dihedral : 18.409 88.584 3314 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.81 % Favored : 97.91 % Rotamer: Outliers : 3.89 % Allowed : 20.53 % Favored : 75.58 % Cbeta Deviations : 0.10 % 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: 1.10 (0.24), residues: 1102 helix: 1.16 (0.18), residues: 744 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 387 TYR 0.028 0.002 TYR C 818 PHE 0.013 0.001 PHE B 87 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.44 ( 9388) covalent geometry : angle 0.95571 / 0.61 (12774) hydrogen bonds : bond 0.16231 / 10.86 ( 575) hydrogen bonds : angle 5.58506 / 4.00 ( 1674) link_ALPHA1-3 : bond 0.01877 / 1.11 ( 2) link_ALPHA1-3 : angle 3.74310 / 1.71 ( 6) link_ALPHA1-4 : bond 0.00243 / 0.15 ( 2) link_ALPHA1-4 : angle 2.37425 / 1.22 ( 6) link_BETA1-4 : bond 0.01987 / 1.38 ( 4) link_BETA1-4 : angle 4.47919 / 2.19 ( 12) link_BETA1-6 : bond 0.00714 / 0.42 ( 2) link_BETA1-6 : angle 0.99506 / 0.52 ( 6) link_NAG-ASN : bond 0.00667 / 0.39 ( 2) link_NAG-ASN : angle 3.94955 / 2.08 ( 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 219 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.382 Fit side-chains REVERT: C 439 GLU cc_start: 0.8841 (mp0) cc_final: 0.8352 (mm-30) REVERT: C 557 VAL cc_start: 0.6589 (OUTLIER) cc_final: 0.6327 (m) REVERT: C 590 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7733 (mtpm) REVERT: C 592 LYS cc_start: 0.8184 (tttm) cc_final: 0.7769 (ttpt) REVERT: E 435 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9095 (mtp) REVERT: E 625 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: E 826 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7360 (mmtp) outliers start: 37 outliers final: 16 residues processed: 206 average time/residue: 0.5414 time to fit residues: 119.6481 Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 810 LEU Chi-restraints excluded: chain E residue 405 VAL Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 672 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN C 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.141220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.118502 restraints weight = 10412.601| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.38 r_work: 0.3112 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9400 Z= 0.127 Angle : 0.589 9.068 12810 Z= 0.282 Chirality : 0.041 0.186 1562 Planarity : 0.006 0.071 1498 Dihedral : 10.767 89.769 1331 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 5.37 % Allowed : 18.63 % Favored : 76.00 % 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 (0.24), residues: 1102 helix: 1.79 (0.19), residues: 750 sheet: None (None), residues: 0 loop : 0.16 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 827 TYR 0.009 0.001 TYR C 824 PHE 0.016 0.001 PHE C 836 TRP 0.011 0.001 TRP C 831 HIS 0.003 0.001 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9388) covalent geometry : angle 0.56924 / 0.28 (12774) hydrogen bonds : bond 0.04772 / 3.25 ( 575) hydrogen bonds : angle 4.39072 / 3.16 ( 1674) link_ALPHA1-3 : bond 0.01633 / 0.96 ( 2) link_ALPHA1-3 : angle 3.96544 / 1.86 ( 6) link_ALPHA1-4 : bond 0.00691 / 0.41 ( 2) link_ALPHA1-4 : angle 2.59166 / 1.26 ( 6) link_BETA1-4 : bond 0.01951 / 1.34 ( 4) link_BETA1-4 : angle 3.67086 / 1.81 ( 12) link_BETA1-6 : bond 0.00630 / 0.37 ( 2) link_BETA1-6 : angle 1.08441 / 0.59 ( 6) link_NAG-ASN : bond 0.00238 / 0.14 ( 2) link_NAG-ASN : angle 1.17278 / 0.60 ( 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 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: C 482 ASN cc_start: 0.7829 (m110) cc_final: 0.7562 (m110) REVERT: C 551 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7543 (tmtm) REVERT: C 564 GLN cc_start: 0.7418 (mm110) cc_final: 0.7181 (mm110) REVERT: C 590 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7700 (mtpm) REVERT: C 672 LEU cc_start: 0.8059 (mt) cc_final: 0.7551 (mm) REVERT: C 757 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7563 (mttt) REVERT: E 541 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8599 (mt) REVERT: E 603 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7718 (mtm-85) REVERT: E 625 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: E 759 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8114 (pp30) outliers start: 51 outliers final: 17 residues processed: 205 average time/residue: 0.5747 time to fit residues: 126.1251 Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 757 LYS Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 877 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 482 ASN C 550 GLN E 569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.136976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113515 restraints weight = 10048.211| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.37 r_work: 0.3053 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9400 Z= 0.178 Angle : 0.618 8.363 12810 Z= 0.295 Chirality : 0.044 0.176 1562 Planarity : 0.006 0.066 1498 Dihedral : 9.960 88.554 1311 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.37 % Allowed : 19.37 % Favored : 75.26 % 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: 1.75 (0.24), residues: 1102 helix: 1.64 (0.18), residues: 758 sheet: None (None), residues: 0 loop : 0.22 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 387 TYR 0.015 0.002 TYR E 824 PHE 0.020 0.002 PHE C 836 TRP 0.013 0.002 TRP C 492 HIS 0.003 0.001 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 9388) covalent geometry : angle 0.60122 / 0.29 (12774) hydrogen bonds : bond 0.05146 / 3.55 ( 575) hydrogen bonds : angle 4.34324 / 3.13 ( 1674) link_ALPHA1-3 : bond 0.01897 / 1.13 ( 2) link_ALPHA1-3 : angle 3.70352 / 1.74 ( 6) link_ALPHA1-4 : bond 0.00850 / 0.51 ( 2) link_ALPHA1-4 : angle 2.09557 / 0.99 ( 6) link_BETA1-4 : bond 0.01925 / 1.33 ( 4) link_BETA1-4 : angle 3.44879 / 1.69 ( 12) link_BETA1-6 : bond 0.00720 / 0.41 ( 2) link_BETA1-6 : angle 1.01227 / 0.52 ( 6) link_NAG-ASN : bond 0.00621 / 0.35 ( 2) link_NAG-ASN : angle 1.87278 / 0.92 ( 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 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: D 107 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7676 (mp) REVERT: C 439 GLU cc_start: 0.8923 (mp0) cc_final: 0.8659 (mp0) REVERT: C 564 GLN cc_start: 0.7486 (mm110) cc_final: 0.7276 (mm110) REVERT: C 672 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7720 (mm) REVERT: C 759 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.6774 (pp30) REVERT: C 827 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8239 (mtp-110) REVERT: E 625 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: E 644 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (p) REVERT: E 759 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8208 (pp30) outliers start: 51 outliers final: 19 residues processed: 197 average time/residue: 0.5564 time to fit residues: 117.5012 Evaluate side-chains 206 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN E 545 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.138632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115339 restraints weight = 10178.673| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.38 r_work: 0.3075 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9400 Z= 0.135 Angle : 0.563 8.215 12810 Z= 0.267 Chirality : 0.042 0.170 1562 Planarity : 0.005 0.061 1498 Dihedral : 9.658 88.453 1308 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.74 % Allowed : 20.21 % Favored : 75.05 % 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: 1.97 (0.24), residues: 1102 helix: 1.81 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.29 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 387 TYR 0.011 0.002 TYR E 824 PHE 0.016 0.001 PHE C 836 TRP 0.012 0.001 TRP C 492 HIS 0.002 0.000 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9388) covalent geometry : angle 0.54549 / 0.26 (12774) hydrogen bonds : bond 0.04495 / 3.10 ( 575) hydrogen bonds : angle 4.22578 / 3.05 ( 1674) link_ALPHA1-3 : bond 0.01777 / 1.06 ( 2) link_ALPHA1-3 : angle 3.62290 / 1.72 ( 6) link_ALPHA1-4 : bond 0.00786 / 0.47 ( 2) link_ALPHA1-4 : angle 2.04150 / 0.98 ( 6) link_BETA1-4 : bond 0.01877 / 1.30 ( 4) link_BETA1-4 : angle 3.32351 / 1.63 ( 12) link_BETA1-6 : bond 0.00630 / 0.37 ( 2) link_BETA1-6 : angle 1.02024 / 0.54 ( 6) link_NAG-ASN : bond 0.00433 / 0.24 ( 2) link_NAG-ASN : angle 1.39247 / 0.68 ( 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 225 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 439 GLU cc_start: 0.8893 (mp0) cc_final: 0.8542 (mp0) REVERT: C 480 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: C 482 ASN cc_start: 0.7907 (m110) cc_final: 0.7572 (m110) REVERT: C 551 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7601 (tmtm) REVERT: C 564 GLN cc_start: 0.7500 (mm110) cc_final: 0.7253 (mm110) REVERT: C 672 LEU cc_start: 0.8159 (mt) cc_final: 0.7839 (tp) REVERT: C 721 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: C 759 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.6676 (pp30) REVERT: E 625 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: E 759 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8007 (pp30) outliers start: 45 outliers final: 16 residues processed: 202 average time/residue: 0.6028 time to fit residues: 129.9720 Evaluate side-chains 201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.138033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.114649 restraints weight = 10141.663| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.38 r_work: 0.3065 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9400 Z= 0.146 Angle : 0.566 7.842 12810 Z= 0.270 Chirality : 0.042 0.186 1562 Planarity : 0.006 0.057 1498 Dihedral : 9.498 88.292 1308 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.05 % Allowed : 20.42 % Favored : 74.53 % 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: 1.97 (0.25), residues: 1102 helix: 1.80 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 387 TYR 0.013 0.002 TYR E 824 PHE 0.017 0.001 PHE C 836 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9388) covalent geometry : angle 0.55042 / 0.27 (12774) hydrogen bonds : bond 0.04567 / 3.16 ( 575) hydrogen bonds : angle 4.22591 / 3.05 ( 1674) link_ALPHA1-3 : bond 0.01757 / 1.05 ( 2) link_ALPHA1-3 : angle 3.59333 / 1.71 ( 6) link_ALPHA1-4 : bond 0.00772 / 0.46 ( 2) link_ALPHA1-4 : angle 1.91024 / 0.92 ( 6) link_BETA1-4 : bond 0.01806 / 1.25 ( 4) link_BETA1-4 : angle 3.18282 / 1.56 ( 12) link_BETA1-6 : bond 0.00642 / 0.37 ( 2) link_BETA1-6 : angle 1.02302 / 0.54 ( 6) link_NAG-ASN : bond 0.00479 / 0.27 ( 2) link_NAG-ASN : angle 1.47909 / 0.71 ( 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 229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 439 GLU cc_start: 0.8909 (mp0) cc_final: 0.8635 (mp0) REVERT: C 480 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 482 ASN cc_start: 0.7879 (m110) cc_final: 0.7563 (m110) REVERT: C 551 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7615 (tmtm) REVERT: C 564 GLN cc_start: 0.7468 (mm110) cc_final: 0.7245 (mm110) REVERT: C 672 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7851 (tp) REVERT: C 759 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.6705 (pp30) REVERT: E 485 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: E 541 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8650 (mt) REVERT: E 625 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: E 759 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8088 (pp30) outliers start: 48 outliers final: 22 residues processed: 200 average time/residue: 0.5813 time to fit residues: 124.2905 Evaluate side-chains 204 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.139211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116008 restraints weight = 10172.902| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.38 r_work: 0.3086 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9400 Z= 0.124 Angle : 0.543 8.766 12810 Z= 0.258 Chirality : 0.041 0.175 1562 Planarity : 0.005 0.054 1498 Dihedral : 9.288 88.442 1308 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 5.58 % Allowed : 19.47 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.34 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 827 TYR 0.011 0.001 TYR E 824 PHE 0.016 0.001 PHE C 836 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS E 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9388) covalent geometry : angle 0.52744 / 0.25 (12774) hydrogen bonds : bond 0.04279 / 2.97 ( 575) hydrogen bonds : angle 4.14437 / 2.99 ( 1674) link_ALPHA1-3 : bond 0.01723 / 1.02 ( 2) link_ALPHA1-3 : angle 3.56864 / 1.69 ( 6) link_ALPHA1-4 : bond 0.00759 / 0.45 ( 2) link_ALPHA1-4 : angle 1.79988 / 0.88 ( 6) link_BETA1-4 : bond 0.01738 / 1.21 ( 4) link_BETA1-4 : angle 3.04603 / 1.49 ( 12) link_BETA1-6 : bond 0.00624 / 0.37 ( 2) link_BETA1-6 : angle 1.00499 / 0.53 ( 6) link_NAG-ASN : bond 0.00380 / 0.21 ( 2) link_NAG-ASN : angle 1.30883 / 0.62 ( 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 231 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 178 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: C 439 GLU cc_start: 0.8882 (mp0) cc_final: 0.8654 (mp0) REVERT: C 480 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: C 482 ASN cc_start: 0.7904 (m110) cc_final: 0.7592 (m110) REVERT: C 551 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7608 (tmtm) REVERT: C 564 GLN cc_start: 0.7473 (mm110) cc_final: 0.7271 (mm110) REVERT: C 592 LYS cc_start: 0.8528 (tttm) cc_final: 0.7947 (ttpt) REVERT: C 759 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.6651 (pp30) REVERT: C 827 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8103 (mtp-110) REVERT: E 430 LYS cc_start: 0.8821 (mttm) cc_final: 0.8527 (mtmt) REVERT: E 485 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: E 541 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (mt) REVERT: E 603 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7699 (mtt-85) REVERT: E 625 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6288 (tm-30) REVERT: E 658 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: E 759 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8056 (pp30) outliers start: 53 outliers final: 18 residues processed: 205 average time/residue: 0.5595 time to fit residues: 122.4691 Evaluate side-chains 201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.137561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.114816 restraints weight = 10291.632| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.37 r_work: 0.3060 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9400 Z= 0.153 Angle : 0.571 7.220 12810 Z= 0.272 Chirality : 0.043 0.203 1562 Planarity : 0.005 0.053 1498 Dihedral : 9.295 88.201 1308 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.42 % Allowed : 20.11 % Favored : 75.47 % 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: 1.98 (0.25), residues: 1102 helix: 1.81 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.32 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 827 TYR 0.013 0.002 TYR E 824 PHE 0.017 0.001 PHE C 836 TRP 0.012 0.001 TRP C 492 HIS 0.002 0.000 HIS E 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9388) covalent geometry : angle 0.55588 / 0.27 (12774) hydrogen bonds : bond 0.04577 / 3.17 ( 575) hydrogen bonds : angle 4.18918 / 3.02 ( 1674) link_ALPHA1-3 : bond 0.01689 / 1.01 ( 2) link_ALPHA1-3 : angle 3.56151 / 1.69 ( 6) link_ALPHA1-4 : bond 0.00743 / 0.44 ( 2) link_ALPHA1-4 : angle 1.70512 / 0.84 ( 6) link_BETA1-4 : bond 0.01660 / 1.16 ( 4) link_BETA1-4 : angle 2.92610 / 1.43 ( 12) link_BETA1-6 : bond 0.00566 / 0.33 ( 2) link_BETA1-6 : angle 1.06673 / 0.57 ( 6) link_NAG-ASN : bond 0.00440 / 0.25 ( 2) link_NAG-ASN : angle 1.79729 / 0.77 ( 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 220 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: C 480 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 482 ASN cc_start: 0.7909 (m110) cc_final: 0.7573 (m110) REVERT: C 551 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7620 (tmtm) REVERT: C 564 GLN cc_start: 0.7512 (mm110) cc_final: 0.7292 (mm110) REVERT: C 672 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 693 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: C 759 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.6691 (pp30) REVERT: E 430 LYS cc_start: 0.8827 (mttm) cc_final: 0.8512 (mtmt) REVERT: E 485 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: E 541 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8677 (mt) REVERT: E 625 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: E 759 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8108 (pp30) outliers start: 42 outliers final: 20 residues processed: 194 average time/residue: 0.5558 time to fit residues: 115.2482 Evaluate side-chains 206 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN E 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.139404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116548 restraints weight = 10308.809| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.39 r_work: 0.3085 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9400 Z= 0.122 Angle : 0.547 9.643 12810 Z= 0.260 Chirality : 0.041 0.184 1562 Planarity : 0.005 0.052 1498 Dihedral : 9.131 88.686 1308 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.00 % Allowed : 20.84 % Favored : 75.16 % 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: 2.11 (0.25), residues: 1102 helix: 1.93 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.32 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 387 TYR 0.010 0.001 TYR E 413 PHE 0.015 0.001 PHE E 471 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS B 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9388) covalent geometry : angle 0.53279 / 0.26 (12774) hydrogen bonds : bond 0.04193 / 2.90 ( 575) hydrogen bonds : angle 4.12410 / 2.98 ( 1674) link_ALPHA1-3 : bond 0.01715 / 1.02 ( 2) link_ALPHA1-3 : angle 3.54534 / 1.68 ( 6) link_ALPHA1-4 : bond 0.00729 / 0.43 ( 2) link_ALPHA1-4 : angle 1.64222 / 0.81 ( 6) link_BETA1-4 : bond 0.01610 / 1.13 ( 4) link_BETA1-4 : angle 2.79404 / 1.36 ( 12) link_BETA1-6 : bond 0.00577 / 0.34 ( 2) link_BETA1-6 : angle 1.03486 / 0.55 ( 6) link_NAG-ASN : bond 0.00324 / 0.18 ( 2) link_NAG-ASN : angle 1.36861 / 0.61 ( 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 221 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: C 480 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: C 482 ASN cc_start: 0.7932 (m110) cc_final: 0.7616 (m110) REVERT: C 551 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7593 (tmtm) REVERT: C 564 GLN cc_start: 0.7512 (mm110) cc_final: 0.7259 (mm110) REVERT: C 592 LYS cc_start: 0.8509 (tttm) cc_final: 0.7947 (ttpt) REVERT: C 672 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8076 (mm) REVERT: C 759 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.6619 (pp30) REVERT: E 430 LYS cc_start: 0.8797 (mttm) cc_final: 0.8477 (mtmt) REVERT: E 434 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8665 (mt0) REVERT: E 485 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: E 541 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8645 (mt) REVERT: E 603 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7716 (mtt-85) REVERT: E 625 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: E 759 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8004 (pp30) outliers start: 38 outliers final: 15 residues processed: 201 average time/residue: 0.5834 time to fit residues: 125.0694 Evaluate side-chains 197 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 541 ILE Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 856 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.139522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116920 restraints weight = 10266.825| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.37 r_work: 0.3088 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9400 Z= 0.122 Angle : 0.546 6.910 12810 Z= 0.261 Chirality : 0.041 0.181 1562 Planarity : 0.005 0.052 1498 Dihedral : 8.991 88.858 1308 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.68 % Allowed : 21.16 % Favored : 75.16 % 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: 2.16 (0.25), residues: 1102 helix: 1.98 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.32 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 827 TYR 0.010 0.001 TYR E 824 PHE 0.016 0.001 PHE C 836 TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9388) covalent geometry : angle 0.53220 / 0.26 (12774) hydrogen bonds : bond 0.04170 / 2.89 ( 575) hydrogen bonds : angle 4.10102 / 2.96 ( 1674) link_ALPHA1-3 : bond 0.01690 / 1.01 ( 2) link_ALPHA1-3 : angle 3.53609 / 1.68 ( 6) link_ALPHA1-4 : bond 0.00721 / 0.43 ( 2) link_ALPHA1-4 : angle 1.59383 / 0.79 ( 6) link_BETA1-4 : bond 0.01562 / 1.09 ( 4) link_BETA1-4 : angle 2.73439 / 1.33 ( 12) link_BETA1-6 : bond 0.00564 / 0.33 ( 2) link_BETA1-6 : angle 1.08623 / 0.57 ( 6) link_NAG-ASN : bond 0.00333 / 0.19 ( 2) link_NAG-ASN : angle 1.35606 / 0.61 ( 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 209 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 480 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: C 482 ASN cc_start: 0.7933 (m110) cc_final: 0.7627 (m110) REVERT: C 551 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7597 (tmtm) REVERT: C 564 GLN cc_start: 0.7510 (mm110) cc_final: 0.7263 (mm110) REVERT: C 592 LYS cc_start: 0.8506 (tttm) cc_final: 0.7927 (ttpt) REVERT: C 672 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8011 (mm) REVERT: C 693 GLU cc_start: 0.7282 (pt0) cc_final: 0.6907 (pm20) REVERT: E 430 LYS cc_start: 0.8816 (mttm) cc_final: 0.8494 (mtmt) REVERT: E 485 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: E 603 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7709 (mtt-85) REVERT: E 625 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6268 (tm-30) REVERT: E 759 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7996 (pp30) outliers start: 35 outliers final: 19 residues processed: 188 average time/residue: 0.5703 time to fit residues: 114.5215 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 779 ILE Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 0.0170 chunk 33 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN E 433 ASN E 434 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.117098 restraints weight = 10275.698| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.37 r_work: 0.3094 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9400 Z= 0.122 Angle : 0.546 10.431 12810 Z= 0.260 Chirality : 0.041 0.177 1562 Planarity : 0.005 0.052 1498 Dihedral : 8.741 88.947 1308 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.26 % Allowed : 21.58 % Favored : 75.16 % 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: 2.18 (0.25), residues: 1102 helix: 1.99 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 827 TYR 0.011 0.001 TYR E 824 PHE 0.015 0.001 PHE C 836 TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9388) covalent geometry : angle 0.53372 / 0.26 (12774) hydrogen bonds : bond 0.04140 / 2.88 ( 575) hydrogen bonds : angle 4.09558 / 2.96 ( 1674) link_ALPHA1-3 : bond 0.01657 / 0.98 ( 2) link_ALPHA1-3 : angle 3.50241 / 1.66 ( 6) link_ALPHA1-4 : bond 0.00705 / 0.42 ( 2) link_ALPHA1-4 : angle 1.50424 / 0.76 ( 6) link_BETA1-4 : bond 0.01478 / 1.04 ( 4) link_BETA1-4 : angle 2.56722 / 1.25 ( 12) link_BETA1-6 : bond 0.00563 / 0.33 ( 2) link_BETA1-6 : angle 1.06143 / 0.56 ( 6) link_NAG-ASN : bond 0.00328 / 0.18 ( 2) link_NAG-ASN : angle 1.29017 / 0.60 ( 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 209 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 480 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: C 482 ASN cc_start: 0.7914 (m110) cc_final: 0.7650 (m110) REVERT: C 551 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7614 (tmtm) REVERT: C 564 GLN cc_start: 0.7513 (mm110) cc_final: 0.7284 (mm110) REVERT: C 592 LYS cc_start: 0.8489 (tttm) cc_final: 0.7909 (ttpt) REVERT: C 672 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8076 (mm) REVERT: C 827 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8073 (mtp-110) REVERT: E 430 LYS cc_start: 0.8783 (mttm) cc_final: 0.8471 (mtmt) REVERT: E 434 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8673 (mt0) REVERT: E 485 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: E 603 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7713 (mtt-85) REVERT: E 625 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: E 658 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: E 759 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7987 (pp30) outliers start: 31 outliers final: 20 residues processed: 190 average time/residue: 0.5627 time to fit residues: 114.0873 Evaluate side-chains 204 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 559 MET Chi-restraints excluded: chain C residue 602 ARG Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain C residue 885 CYS Chi-restraints excluded: chain E residue 434 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 485 GLU Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 658 GLU Chi-restraints excluded: chain E residue 661 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 697 VAL Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 779 ILE Chi-restraints excluded: chain E residue 856 SER Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 550 GLN C 884 GLN E 434 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.139800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117076 restraints weight = 10191.084| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.38 r_work: 0.3090 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 9400 Z= 0.238 Angle : 0.895 59.199 12810 Z= 0.505 Chirality : 0.042 0.333 1562 Planarity : 0.005 0.052 1498 Dihedral : 8.776 88.950 1308 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.05 % Allowed : 21.89 % Favored : 75.05 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2.16 (0.25), residues: 1102 helix: 1.99 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.28 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 827 TYR 0.011 0.001 TYR E 824 PHE 0.015 0.001 PHE C 836 TRP 0.012 0.001 TRP C 492 HIS 0.001 0.000 HIS C 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.24 ( 9388) covalent geometry : angle 0.88861 / 0.50 (12774) hydrogen bonds : bond 0.04136 / 2.87 ( 575) hydrogen bonds : angle 4.09479 / 2.96 ( 1674) link_ALPHA1-3 : bond 0.01662 / 0.99 ( 2) link_ALPHA1-3 : angle 3.51491 / 1.67 ( 6) link_ALPHA1-4 : bond 0.00705 / 0.42 ( 2) link_ALPHA1-4 : angle 1.50368 / 0.76 ( 6) link_BETA1-4 : bond 0.01489 / 1.05 ( 4) link_BETA1-4 : angle 2.57299 / 1.25 ( 12) link_BETA1-6 : bond 0.00564 / 0.33 ( 2) link_BETA1-6 : angle 1.06405 / 0.57 ( 6) link_NAG-ASN : bond 0.00328 / 0.18 ( 2) link_NAG-ASN : angle 1.29337 / 0.60 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.86 seconds wall clock time: 67 minutes 25.89 seconds (4045.89 seconds total)