Starting phenix.real_space_refine on Fri Jul 3 22:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mos_48480/07_2026/9mos_48480_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mos_48480/07_2026/9mos_48480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mos_48480/07_2026/9mos_48480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mos_48480/07_2026/9mos_48480.map" model { file = "/net/cci-nas-00/data/ceres_data/9mos_48480/07_2026/9mos_48480_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mos_48480/07_2026/9mos_48480_trim.cif" } resolution = 2.88 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= 0.055 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 S 34 5.16 5 Cl 1 4.86 5 C 5260 2.51 5 N 1212 2.21 5 O 1344 1.98 5 H 7927 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 15786 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 8240 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 510, 8228 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 28, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 510, 8228 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 28, 'TRANS': 481} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 8317 Chain: "A" Number of atoms: 7269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7269 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PIO': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 613 " occ=0.54 ... (20 atoms not shown) pdb=" HG BSER C 613 " occ=0.46 Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15786 At special positions: 0 Unit cell: (83.6785, 83.6785, 122.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 34 16.00 P 8 15.00 O 1344 8.00 N 1212 7.00 C 5260 6.00 H 7927 1.00 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 ALPHA1-6 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 5 " NAG-ASN " NAG B 1 " - " ASN C 642 " " NAG D 1 " - " ASN A 642 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 639.1 milliseconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 75.9% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 402 through 431 removed outlier: 3.813A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 465 through 483 Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.561A pdb=" N VAL C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 517 through 547 Processing helix chain 'C' and resid 569 through 593 removed outlier: 3.656A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 609 through 623 Processing helix chain 'C' and resid 660 through 667 removed outlier: 3.548A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 701 through 720 Processing helix chain 'C' and resid 727 through 738 Processing helix chain 'C' and resid 760 through 774 removed outlier: 3.627A pdb=" N LEU C 764 " --> pdb=" O ARG C 760 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 774 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 784 through 800 removed outlier: 3.619A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 815 through 819 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 878 removed outlier: 4.293A pdb=" N LEU C 874 " --> pdb=" O ARG C 870 " (cutoff:3.500A) Proline residue: C 875 - end of helix Processing helix chain 'C' and resid 879 through 887 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.542A pdb=" N PHE A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.686A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.771A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 687 Processing helix chain 'A' and resid 702 through 718 removed outlier: 3.871A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.598A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 813 through 814 No H-bonds generated for 'chain 'A' and resid 813 through 814' Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.667A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 878 removed outlier: 3.561A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 463 removed outlier: 3.560A pdb=" N SER C 725 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 739 through 740 removed outlier: 3.731A pdb=" N GLU C 755 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 460 through 463 removed outlier: 6.822A pdb=" N VAL A 461 " --> pdb=" O THR A 727 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1525 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: 3.27 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7921 1.03 - 1.23: 18 1.23 - 1.42: 3229 1.42 - 1.62: 4736 1.62 - 1.81: 74 Bond restraints: 15978 Sorted by residual: bond pdb=" C1B PIO C1001 " pdb=" O3C PIO C1001 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1A PIO C1001 " pdb=" O2C PIO C1001 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1B PIO A1002 " pdb=" O3C PIO A1002 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1A PIO A1002 " pdb=" O2C PIO A1002 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O4 PIO C1001 " pdb=" P4 PIO C1001 " ideal model delta sigma weight residual 1.710 1.646 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 15973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 28761 2.56 - 5.12: 147 5.12 - 7.68: 23 7.68 - 10.24: 6 10.24 - 12.80: 4 Bond angle restraints: 28941 Sorted by residual: angle pdb=" O1 PIO C1001 " pdb=" P1 PIO C1001 " pdb=" O13 PIO C1001 " ideal model delta sigma weight residual 97.64 110.44 -12.80 3.00e+00 1.11e-01 1.82e+01 angle pdb=" O11 PIO C1001 " pdb=" P1 PIO C1001 " pdb=" O12 PIO C1001 " ideal model delta sigma weight residual 121.09 109.18 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 PIO A1002 " pdb=" P1 PIO A1002 " pdb=" O12 PIO A1002 " ideal model delta sigma weight residual 121.09 109.67 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O1 PIO A1002 " pdb=" P1 PIO A1002 " pdb=" O13 PIO A1002 " ideal model delta sigma weight residual 97.64 109.05 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C2A PIO A1002 " pdb=" C1A PIO A1002 " pdb=" O2C PIO A1002 " ideal model delta sigma weight residual 110.66 120.37 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 28936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.99: 7065 26.99 - 53.98: 468 53.98 - 80.98: 79 80.98 - 107.97: 10 107.97 - 134.96: 2 Dihedral angle restraints: 7624 sinusoidal: 4208 harmonic: 3416 Sorted by residual: dihedral pdb=" C3 PLC A1001 " pdb=" C1 PLC A1001 " pdb=" C2 PLC A1001 " pdb=" O3P PLC A1001 " ideal model delta sinusoidal sigma weight residual 67.16 -157.88 -134.96 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" O2 PLC A1001 " pdb=" C1 PLC A1001 " pdb=" C2 PLC A1001 " pdb=" O3P PLC A1001 " ideal model delta sinusoidal sigma weight residual -55.71 76.32 -132.03 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" O2 PLC C1002 " pdb=" C1 PLC C1002 " pdb=" C2 PLC C1002 " pdb=" O3P PLC C1002 " ideal model delta sinusoidal sigma weight residual -55.71 -152.64 96.93 1 3.00e+01 1.11e-03 1.20e+01 ... (remaining 7621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 988 0.039 - 0.077: 254 0.077 - 0.116: 76 0.116 - 0.154: 9 0.154 - 0.193: 1 Chirality restraints: 1328 Sorted by residual: chirality pdb=" C5 PIO C1001 " pdb=" C4 PIO C1001 " pdb=" C6 PIO C1001 " pdb=" O5 PIO C1001 " both_signs ideal model delta sigma weight residual False -2.47 -2.27 -0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" C5 PIO A1002 " pdb=" C4 PIO A1002 " pdb=" C6 PIO A1002 " pdb=" O5 PIO A1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.32 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE A 624 " pdb=" N ILE A 624 " pdb=" C ILE A 624 " pdb=" CB ILE A 624 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1325 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 874 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 875 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 875 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 875 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 597 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO C 598 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 598 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 598 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 867 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO C 868 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 868 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 868 " 0.020 5.00e-02 4.00e+02 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 6471 2.39 - 2.94: 36436 2.94 - 3.50: 43515 3.50 - 4.05: 56809 4.05 - 4.60: 85147 Nonbonded interactions: 228378 Sorted by model distance: nonbonded pdb=" H GLU C 508 " pdb=" HG2 GLU C 508 " model vdw 1.840 2.270 nonbonded pdb="HE21 GLN C 457 " pdb=" H LEU C 459 " model vdw 1.871 2.100 nonbonded pdb=" HE1 PHE A 423 " pdb=" HE1 PHE A 792 " model vdw 1.881 2.100 nonbonded pdb=" HG1 THR C 520 " pdb=" HG1 THR C 866 " model vdw 1.891 2.100 nonbonded pdb=" HD2 ARG C 490 " pdb="HH11 ARG C 490 " model vdw 1.916 2.270 ... (remaining 228373 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' and (resid 400 through 599 or (resid 600 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 601 through 612 or re \ sid 615 through 751 or (resid 753 and (name N or name CA or name C or name O or \ name CB or name HA )) or resid 754 through 1001)) selection = (chain 'C' and ((resid 400 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 401 through 403 or (r \ esid 404 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 405 through 504 or (resid 505 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 506 or (resid 507 through 5 \ 08 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 509 or (resid 510 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 511 through 513 or (resid 514 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 515 thro \ ugh 612 or resid 615 through 684 or (resid 685 through 687 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or (resid 701 and (name \ N or name CA or name C or name O or name HA2 or name HA3)) or resid 702 through \ 730 or (resid 731 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or (resid 737 and (name N or name CA or name C or name O or nam \ e CB or name HA or name HB1 or name HB2 or name HB3)) or (resid 753 and (name N \ or name CA or name C or name O or name CB or name HA )) or (resid 754 through 75 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 756 or (resid 757 through 758 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 759 through 890 or resid 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.730 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: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.050 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8059 Z= 0.179 Angle : 0.751 12.795 10973 Z= 0.335 Chirality : 0.039 0.193 1328 Planarity : 0.005 0.045 1302 Dihedral : 18.319 134.959 3024 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.97 % Allowed : 27.86 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.73 (0.28), residues: 962 helix: 1.78 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.23 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.013 0.001 TYR C 486 PHE 0.015 0.001 PHE C 471 TRP 0.010 0.001 TRP A 492 HIS 0.002 0.001 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 ( 8051) covalent geometry : angle 0.74474 / 0.33 (10949) hydrogen bonds : bond 0.09978 / 7.15 ( 519) hydrogen bonds : angle 5.14322 / 3.59 ( 1525) link_ALPHA1-6 : bond 0.00980 / 0.65 ( 1) link_ALPHA1-6 : angle 1.56994 / 0.99 ( 3) link_BETA1-4 : bond 0.00404 / 0.23 ( 3) link_BETA1-4 : angle 2.17256 / 1.22 ( 9) link_BETA1-6 : bond 0.00615 / 0.43 ( 2) link_BETA1-6 : angle 1.12510 / 0.74 ( 6) link_NAG-ASN : bond 0.00333 / 0.24 ( 2) link_NAG-ASN : angle 3.14167 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.432 Fit side-chains REVERT: C 741 MET cc_start: 0.5746 (tmt) cc_final: 0.5251 (tmt) REVERT: C 879 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7194 (mmt-90) REVERT: A 833 MET cc_start: 0.8638 (ttp) cc_final: 0.8434 (ttp) REVERT: A 871 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7535 (mmp-170) REVERT: A 879 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.6980 (mmp-170) outliers start: 7 outliers final: 7 residues processed: 80 average time/residue: 1.0390 time to fit residues: 89.2459 Evaluate side-chains 72 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 636 ASP Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 703 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098517 restraints weight = 44102.372| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.02 r_work: 0.3188 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8059 Z= 0.179 Angle : 0.586 7.522 10973 Z= 0.287 Chirality : 0.040 0.197 1328 Planarity : 0.005 0.050 1302 Dihedral : 10.695 106.581 1307 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.19 % Allowed : 25.30 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 962 helix: 1.83 (0.20), residues: 677 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.013 0.001 TYR C 824 PHE 0.015 0.001 PHE C 792 TRP 0.009 0.001 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 8051) covalent geometry : angle 0.57755 / 0.28 (10949) hydrogen bonds : bond 0.04936 / 3.28 ( 519) hydrogen bonds : angle 4.52930 / 3.23 ( 1525) link_ALPHA1-6 : bond 0.00731 / 0.49 ( 1) link_ALPHA1-6 : angle 1.26228 / 0.92 ( 3) link_BETA1-4 : bond 0.00234 / 0.11 ( 3) link_BETA1-4 : angle 2.06656 / 1.19 ( 9) link_BETA1-6 : bond 0.00587 / 0.41 ( 2) link_BETA1-6 : angle 1.14452 / 0.70 ( 6) link_NAG-ASN : bond 0.00272 / 0.18 ( 2) link_NAG-ASN : angle 3.34002 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.454 Fit side-chains REVERT: C 741 MET cc_start: 0.5574 (tmt) cc_final: 0.5139 (tmt) REVERT: C 879 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7028 (mmt180) REVERT: A 457 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7937 (tp40) REVERT: A 833 MET cc_start: 0.8840 (ttp) cc_final: 0.8624 (ttp) REVERT: A 879 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7126 (mmp-170) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 1.1167 time to fit residues: 99.5366 Evaluate side-chains 73 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 703 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 840 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099162 restraints weight = 42602.642| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.00 r_work: 0.3198 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8059 Z= 0.151 Angle : 0.560 7.810 10973 Z= 0.273 Chirality : 0.039 0.157 1328 Planarity : 0.005 0.049 1302 Dihedral : 9.905 101.151 1302 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.95 % Allowed : 24.45 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.27), residues: 962 helix: 1.87 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 808 TYR 0.012 0.001 TYR C 824 PHE 0.014 0.001 PHE C 792 TRP 0.009 0.001 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8051) covalent geometry : angle 0.55185 / 0.27 (10949) hydrogen bonds : bond 0.04696 / 3.13 ( 519) hydrogen bonds : angle 4.37226 / 3.11 ( 1525) link_ALPHA1-6 : bond 0.00671 / 0.45 ( 1) link_ALPHA1-6 : angle 1.28233 / 0.92 ( 3) link_BETA1-4 : bond 0.00203 / 0.10 ( 3) link_BETA1-4 : angle 1.79338 / 1.07 ( 9) link_BETA1-6 : bond 0.00600 / 0.42 ( 2) link_BETA1-6 : angle 1.22832 / 0.75 ( 6) link_NAG-ASN : bond 0.00271 / 0.19 ( 2) link_NAG-ASN : angle 3.16815 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.468 Fit side-chains REVERT: C 741 MET cc_start: 0.5656 (tmt) cc_final: 0.5288 (tmt) REVERT: C 879 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7006 (mmt180) REVERT: A 829 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7921 (mttp) REVERT: A 833 MET cc_start: 0.8819 (ttp) cc_final: 0.8616 (ttp) REVERT: A 879 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7226 (mmp-170) outliers start: 14 outliers final: 7 residues processed: 76 average time/residue: 1.1354 time to fit residues: 92.5581 Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099212 restraints weight = 45633.502| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.06 r_work: 0.3195 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8059 Z= 0.149 Angle : 0.551 7.454 10973 Z= 0.268 Chirality : 0.038 0.153 1328 Planarity : 0.005 0.049 1302 Dihedral : 9.584 90.148 1300 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.19 % Allowed : 23.11 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.99 (0.27), residues: 962 helix: 1.99 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -0.34 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.015 0.001 TYR C 390 PHE 0.013 0.001 PHE C 792 TRP 0.009 0.001 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8051) covalent geometry : angle 0.54418 / 0.27 (10949) hydrogen bonds : bond 0.04513 / 2.99 ( 519) hydrogen bonds : angle 4.25753 / 3.03 ( 1525) link_ALPHA1-6 : bond 0.00593 / 0.40 ( 1) link_ALPHA1-6 : angle 1.29634 / 0.95 ( 3) link_BETA1-4 : bond 0.00281 / 0.14 ( 3) link_BETA1-4 : angle 1.62614 / 1.01 ( 9) link_BETA1-6 : bond 0.00581 / 0.40 ( 2) link_BETA1-6 : angle 1.15663 / 0.70 ( 6) link_NAG-ASN : bond 0.00342 / 0.24 ( 2) link_NAG-ASN : angle 3.10127 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.358 Fit side-chains REVERT: C 434 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: C 741 MET cc_start: 0.5689 (tmt) cc_final: 0.5395 (tmt) REVERT: C 879 ARG cc_start: 0.7574 (mtm110) cc_final: 0.6972 (mmt180) REVERT: A 829 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7916 (mttp) REVERT: A 833 MET cc_start: 0.8817 (ttp) cc_final: 0.8609 (ttp) REVERT: A 879 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7218 (mmp-170) REVERT: A 884 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7760 (tp-100) outliers start: 16 outliers final: 6 residues processed: 79 average time/residue: 1.0178 time to fit residues: 86.5820 Evaluate side-chains 73 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099079 restraints weight = 47980.206| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.11 r_work: 0.3189 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8059 Z= 0.149 Angle : 0.546 7.324 10973 Z= 0.267 Chirality : 0.038 0.133 1328 Planarity : 0.005 0.050 1302 Dihedral : 9.538 86.458 1300 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.95 % Allowed : 23.11 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.00 (0.27), residues: 962 helix: 2.00 (0.20), residues: 685 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 389 TYR 0.012 0.001 TYR C 824 PHE 0.013 0.001 PHE C 792 TRP 0.009 0.001 TRP A 492 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8051) covalent geometry : angle 0.53919 / 0.27 (10949) hydrogen bonds : bond 0.04509 / 2.99 ( 519) hydrogen bonds : angle 4.22496 / 3.01 ( 1525) link_ALPHA1-6 : bond 0.00565 / 0.38 ( 1) link_ALPHA1-6 : angle 1.30806 / 0.96 ( 3) link_BETA1-4 : bond 0.00245 / 0.12 ( 3) link_BETA1-4 : angle 1.56863 / 1.00 ( 9) link_BETA1-6 : bond 0.00538 / 0.37 ( 2) link_BETA1-6 : angle 1.16378 / 0.70 ( 6) link_NAG-ASN : bond 0.00293 / 0.20 ( 2) link_NAG-ASN : angle 3.11064 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.448 Fit side-chains REVERT: C 434 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: C 741 MET cc_start: 0.5590 (tmt) cc_final: 0.5279 (tmt) REVERT: C 879 ARG cc_start: 0.7533 (mtm110) cc_final: 0.6884 (mmt180) REVERT: A 829 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7892 (mttp) REVERT: A 833 MET cc_start: 0.8833 (ttp) cc_final: 0.8610 (ttp) REVERT: A 879 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7127 (mmp-170) REVERT: A 884 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7735 (tp-100) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.9790 time to fit residues: 80.1742 Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097576 restraints weight = 46769.067| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.09 r_work: 0.3165 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8059 Z= 0.208 Angle : 0.576 6.042 10973 Z= 0.285 Chirality : 0.040 0.138 1328 Planarity : 0.005 0.052 1302 Dihedral : 9.778 85.509 1300 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.19 % Allowed : 22.38 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.79 (0.27), residues: 962 helix: 1.86 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.015 0.002 TYR C 390 PHE 0.015 0.002 PHE C 702 TRP 0.009 0.001 TRP A 492 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 8051) covalent geometry : angle 0.56820 / 0.28 (10949) hydrogen bonds : bond 0.04891 / 3.24 ( 519) hydrogen bonds : angle 4.32788 / 3.08 ( 1525) link_ALPHA1-6 : bond 0.00520 / 0.35 ( 1) link_ALPHA1-6 : angle 1.31388 / 0.96 ( 3) link_BETA1-4 : bond 0.00194 / 0.11 ( 3) link_BETA1-4 : angle 1.64375 / 1.08 ( 9) link_BETA1-6 : bond 0.00650 / 0.45 ( 2) link_BETA1-6 : angle 1.14811 / 0.67 ( 6) link_NAG-ASN : bond 0.00338 / 0.23 ( 2) link_NAG-ASN : angle 3.47627 / 1.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.426 Fit side-chains REVERT: C 434 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: C 688 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8241 (mm) REVERT: C 741 MET cc_start: 0.5575 (tmt) cc_final: 0.5234 (tmt) REVERT: C 879 ARG cc_start: 0.7551 (mtm110) cc_final: 0.6852 (mmt180) REVERT: A 829 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7947 (mttm) REVERT: A 833 MET cc_start: 0.8862 (ttp) cc_final: 0.8638 (ttp) REVERT: A 879 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7106 (mmp-170) REVERT: A 884 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7755 (tp-100) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 1.0454 time to fit residues: 84.2676 Evaluate side-chains 73 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 633 SER Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098872 restraints weight = 47872.690| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.13 r_work: 0.3190 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8059 Z= 0.133 Angle : 0.532 5.599 10973 Z= 0.262 Chirality : 0.038 0.131 1328 Planarity : 0.005 0.050 1302 Dihedral : 9.437 88.235 1300 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.58 % Allowed : 22.63 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.02 (0.27), residues: 962 helix: 2.01 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 389 TYR 0.010 0.001 TYR C 486 PHE 0.014 0.001 PHE C 471 TRP 0.010 0.001 TRP A 492 HIS 0.002 0.001 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8051) covalent geometry : angle 0.52494 / 0.26 (10949) hydrogen bonds : bond 0.04405 / 2.91 ( 519) hydrogen bonds : angle 4.18731 / 2.98 ( 1525) link_ALPHA1-6 : bond 0.00548 / 0.37 ( 1) link_ALPHA1-6 : angle 1.32038 / 0.99 ( 3) link_BETA1-4 : bond 0.00304 / 0.17 ( 3) link_BETA1-4 : angle 1.45916 / 0.95 ( 9) link_BETA1-6 : bond 0.00527 / 0.36 ( 2) link_BETA1-6 : angle 1.20096 / 0.73 ( 6) link_NAG-ASN : bond 0.00316 / 0.22 ( 2) link_NAG-ASN : angle 3.03820 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.425 Fit side-chains REVERT: C 434 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: C 688 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8219 (mm) REVERT: C 741 MET cc_start: 0.5738 (tmt) cc_final: 0.5480 (tmt) REVERT: C 879 ARG cc_start: 0.7528 (mtm110) cc_final: 0.6892 (mmt180) REVERT: A 829 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7931 (mttp) REVERT: A 833 MET cc_start: 0.8820 (ttp) cc_final: 0.8607 (ttp) REVERT: A 879 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7224 (mmp-170) REVERT: A 884 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7776 (tp-100) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 1.0395 time to fit residues: 80.4642 Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099364 restraints weight = 42474.129| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.00 r_work: 0.3203 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8059 Z= 0.132 Angle : 0.520 4.995 10973 Z= 0.258 Chirality : 0.037 0.132 1328 Planarity : 0.005 0.049 1302 Dihedral : 9.233 81.919 1300 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.34 % Allowed : 23.11 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.14 (0.27), residues: 962 helix: 2.17 (0.20), residues: 679 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 490 TYR 0.015 0.001 TYR C 390 PHE 0.013 0.001 PHE C 411 TRP 0.011 0.001 TRP A 492 HIS 0.002 0.000 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8051) covalent geometry : angle 0.51315 / 0.26 (10949) hydrogen bonds : bond 0.04342 / 2.87 ( 519) hydrogen bonds : angle 4.13262 / 2.94 ( 1525) link_ALPHA1-6 : bond 0.00542 / 0.36 ( 1) link_ALPHA1-6 : angle 1.34623 / 1.01 ( 3) link_BETA1-4 : bond 0.00267 / 0.14 ( 3) link_BETA1-4 : angle 1.46317 / 0.97 ( 9) link_BETA1-6 : bond 0.00543 / 0.37 ( 2) link_BETA1-6 : angle 1.13551 / 0.68 ( 6) link_NAG-ASN : bond 0.00275 / 0.19 ( 2) link_NAG-ASN : angle 2.98208 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.383 Fit side-chains REVERT: C 434 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: C 688 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8212 (mm) REVERT: C 741 MET cc_start: 0.5728 (tmt) cc_final: 0.5491 (tmt) REVERT: C 879 ARG cc_start: 0.7505 (mtm110) cc_final: 0.6873 (mmt180) REVERT: A 829 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7919 (mttp) REVERT: A 833 MET cc_start: 0.8801 (ttp) cc_final: 0.8588 (ttp) REVERT: A 879 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7228 (mmp-170) REVERT: A 884 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7775 (tp-100) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 1.1538 time to fit residues: 84.3348 Evaluate side-chains 69 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099148 restraints weight = 46966.836| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.09 r_work: 0.3205 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8059 Z= 0.123 Angle : 0.509 4.779 10973 Z= 0.253 Chirality : 0.037 0.132 1328 Planarity : 0.005 0.049 1302 Dihedral : 8.848 73.133 1300 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.46 % Allowed : 22.87 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.24 (0.27), residues: 962 helix: 2.23 (0.20), residues: 681 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 490 TYR 0.012 0.001 TYR C 390 PHE 0.014 0.001 PHE C 411 TRP 0.014 0.001 TRP A 492 HIS 0.002 0.001 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8051) covalent geometry : angle 0.50265 / 0.25 (10949) hydrogen bonds : bond 0.04201 / 2.78 ( 519) hydrogen bonds : angle 4.06679 / 2.89 ( 1525) link_ALPHA1-6 : bond 0.00546 / 0.36 ( 1) link_ALPHA1-6 : angle 1.35141 / 1.02 ( 3) link_BETA1-4 : bond 0.00265 / 0.16 ( 3) link_BETA1-4 : angle 1.37218 / 0.91 ( 9) link_BETA1-6 : bond 0.00484 / 0.33 ( 2) link_BETA1-6 : angle 1.13794 / 0.68 ( 6) link_NAG-ASN : bond 0.00275 / 0.20 ( 2) link_NAG-ASN : angle 2.85819 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.518 Fit side-chains REVERT: C 434 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: C 688 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8214 (mm) REVERT: C 741 MET cc_start: 0.5832 (tmt) cc_final: 0.5610 (tmt) REVERT: C 879 ARG cc_start: 0.7520 (mtm110) cc_final: 0.6882 (mmt180) REVERT: A 829 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7920 (mttp) REVERT: A 833 MET cc_start: 0.8799 (ttp) cc_final: 0.8590 (ttp) REVERT: A 879 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7238 (mmp-170) REVERT: A 884 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7767 (tp-100) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 1.0111 time to fit residues: 77.1365 Evaluate side-chains 71 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099990 restraints weight = 39905.070| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.90 r_work: 0.3228 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8059 Z= 0.119 Angle : 0.505 4.751 10973 Z= 0.250 Chirality : 0.037 0.132 1328 Planarity : 0.005 0.049 1302 Dihedral : 8.640 74.753 1300 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.34 % Allowed : 23.11 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.32 (0.27), residues: 962 helix: 2.30 (0.20), residues: 681 sheet: None (None), residues: 0 loop : -0.39 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 389 TYR 0.009 0.001 TYR C 534 PHE 0.013 0.001 PHE C 411 TRP 0.013 0.001 TRP A 492 HIS 0.002 0.000 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8051) covalent geometry : angle 0.49845 / 0.25 (10949) hydrogen bonds : bond 0.04130 / 2.74 ( 519) hydrogen bonds : angle 4.01782 / 2.86 ( 1525) link_ALPHA1-6 : bond 0.00531 / 0.35 ( 1) link_ALPHA1-6 : angle 1.37614 / 1.04 ( 3) link_BETA1-4 : bond 0.00280 / 0.16 ( 3) link_BETA1-4 : angle 1.36786 / 0.90 ( 9) link_BETA1-6 : bond 0.00515 / 0.35 ( 2) link_BETA1-6 : angle 1.12261 / 0.68 ( 6) link_NAG-ASN : bond 0.00255 / 0.18 ( 2) link_NAG-ASN : angle 2.81747 / 1.31 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 402 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue VAL 505 is missing expected H atoms. Skipping. Residue SER 510 is missing expected H atoms. Skipping. Residue THR 685 is missing expected H atoms. Skipping. Residue THR 686 is missing expected H atoms. Skipping. Residue LEU 687 is missing expected H atoms. Skipping. Residue SER 731 is missing expected H atoms. Skipping. Residue ILE 753 is missing expected H atoms. Skipping. Residue LYS 757 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.382 Fit side-chains REVERT: C 434 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: C 688 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (mm) REVERT: C 741 MET cc_start: 0.5852 (tmt) cc_final: 0.5526 (tmt) REVERT: C 879 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6917 (mmt180) REVERT: A 829 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7878 (mttt) REVERT: A 833 MET cc_start: 0.8770 (ttp) cc_final: 0.8564 (ttp) REVERT: A 879 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7286 (mmp-170) REVERT: A 884 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7764 (tp-100) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 1.1929 time to fit residues: 89.4687 Evaluate side-chains 72 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 829 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098997 restraints weight = 48905.325| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.09 r_work: 0.3206 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8059 Z= 0.125 Angle : 0.505 4.765 10973 Z= 0.251 Chirality : 0.037 0.132 1328 Planarity : 0.005 0.049 1302 Dihedral : 8.645 78.311 1300 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.46 % Allowed : 22.99 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 2.33 (0.27), residues: 962 helix: 2.32 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -0.41 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 389 TYR 0.015 0.001 TYR C 390 PHE 0.013 0.001 PHE C 411 TRP 0.013 0.001 TRP A 492 HIS 0.002 0.000 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8051) covalent geometry : angle 0.49873 / 0.25 (10949) hydrogen bonds : bond 0.04161 / 2.75 ( 519) hydrogen bonds : angle 4.01220 / 2.85 ( 1525) link_ALPHA1-6 : bond 0.00489 / 0.33 ( 1) link_ALPHA1-6 : angle 1.34700 / 1.02 ( 3) link_BETA1-4 : bond 0.00291 / 0.16 ( 3) link_BETA1-4 : angle 1.36942 / 0.90 ( 9) link_BETA1-6 : bond 0.00509 / 0.35 ( 2) link_BETA1-6 : angle 1.11100 / 0.66 ( 6) link_NAG-ASN : bond 0.00254 / 0.18 ( 2) link_NAG-ASN : angle 2.84968 / 1.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5186.27 seconds wall clock time: 88 minutes 28.75 seconds (5308.75 seconds total)