Starting phenix.real_space_refine on Fri Sep 11 10:02:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.map" model { file = "/net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8crr_26956/09_2026/8crr_26956.cif" } resolution = 3.0 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= 0.154 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 5968 2.51 5 N 1408 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8936 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.97, per 1000 atoms: 0.22 Number of scatterers: 8936 At special positions: 0 Unit cell: (104.165, 109.145, 126.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1516 8.00 N 1408 7.00 C 5968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 239.5 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 74.6% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 88 through 114 Processing helix chain 'D' and resid 88 through 114 Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 402 through 431 removed outlier: 3.564A pdb=" N LEU C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 465 through 482 Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.620A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 516 removed outlier: 3.504A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 547 removed outlier: 3.601A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 594 removed outlier: 3.747A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'C' and resid 660 through 667 removed outlier: 3.600A pdb=" N MET C 664 " --> pdb=" O PRO C 660 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 690 Processing helix chain 'C' and resid 691 through 695 Processing helix chain 'C' and resid 701 through 718 removed outlier: 3.755A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 738 Processing helix chain 'C' and resid 760 through 772 Processing helix chain 'C' and resid 776 through 781 Processing helix chain 'C' and resid 784 through 799 removed outlier: 3.739A pdb=" N LEU C 788 " --> pdb=" O PRO C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.513A pdb=" N LEU C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 814 No H-bonds generated for 'chain 'C' and resid 813 through 814' Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 822 through 827 Processing helix chain 'C' and resid 829 through 852 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 858 through 865 Processing helix chain 'C' and resid 865 through 872 Processing helix chain 'C' and resid 873 through 877 Processing helix chain 'C' and resid 879 through 887 Processing helix chain 'E' and resid 379 through 390 Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 402 through 432 removed outlier: 3.614A pdb=" N LEU E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 436 through 455 Processing helix chain 'E' and resid 465 through 483 Processing helix chain 'E' and resid 485 through 507 removed outlier: 3.606A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.686A pdb=" N VAL E 513 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 547 removed outlier: 3.538A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 594 removed outlier: 3.706A pdb=" N ASN E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 608 Processing helix chain 'E' and resid 608 through 623 Processing helix chain 'E' and resid 660 through 667 removed outlier: 3.571A pdb=" N MET E 664 " --> pdb=" O PRO E 660 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 667 through 690 Processing helix chain 'E' and resid 691 through 695 removed outlier: 3.565A pdb=" N LYS E 695 " --> pdb=" O PRO E 692 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 719 removed outlier: 3.661A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 719 " --> pdb=" O VAL E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 738 Processing helix chain 'E' and resid 760 through 772 Processing helix chain 'E' and resid 776 through 781 Processing helix chain 'E' and resid 784 through 799 removed outlier: 3.748A pdb=" N LEU E 788 " --> pdb=" O PRO E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 803 through 811 Processing helix chain 'E' and resid 812 through 814 No H-bonds generated for 'chain 'E' and resid 812 through 814' Processing helix chain 'E' and resid 815 through 819 Processing helix chain 'E' and resid 822 through 827 Processing helix chain 'E' and resid 829 through 852 Processing helix chain 'E' and resid 855 through 857 No H-bonds generated for 'chain 'E' and resid 855 through 857' Processing helix chain 'E' and resid 858 through 865 Processing helix chain 'E' and resid 865 through 872 Processing helix chain 'E' and resid 873 through 878 removed outlier: 3.764A pdb=" N ILE E 877 " --> pdb=" O LEU E 873 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'C' and resid 461 through 463 removed outlier: 4.957A pdb=" N VAL C 461 " --> pdb=" O THR C 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 739 through 741 Processing sheet with id=AA3, first strand: chain 'E' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'E' and resid 739 through 741 576 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.43: 2439 1.43 - 1.56: 5331 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9158 Sorted by residual: bond pdb=" C1A PIO C1002 " pdb=" O2C PIO C1002 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1B PIO E1002 " pdb=" O3C PIO E1002 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1B PIO C1002 " pdb=" O3C PIO C1002 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O4 PIO E1002 " pdb=" P4 PIO E1002 " ideal model delta sigma weight residual 1.710 1.645 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O4 PIO C1002 " pdb=" P4 PIO C1002 " ideal model delta sigma weight residual 1.710 1.646 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 12278 2.49 - 4.99: 142 4.99 - 7.48: 32 7.48 - 9.97: 6 9.97 - 12.47: 4 Bond angle restraints: 12462 Sorted by residual: angle pdb=" O1 PIO E1002 " pdb=" P1 PIO E1002 " pdb=" O13 PIO E1002 " ideal model delta sigma weight residual 97.64 110.11 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" O11 PIO E1002 " pdb=" P1 PIO E1002 " pdb=" O12 PIO E1002 " ideal model delta sigma weight residual 121.09 109.09 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1 PIO C1002 " pdb=" P1 PIO C1002 " pdb=" O13 PIO C1002 " ideal model delta sigma weight residual 97.64 109.52 -11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 PIO C1002 " pdb=" P1 PIO C1002 " pdb=" O12 PIO C1002 " ideal model delta sigma weight residual 121.09 109.52 11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C2A PIO C1002 " pdb=" C1A PIO C1002 " pdb=" O2C PIO C1002 " ideal model delta sigma weight residual 110.66 120.58 -9.92 3.00e+00 1.11e-01 1.09e+01 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5002 17.86 - 35.72: 245 35.72 - 53.58: 50 53.58 - 71.44: 11 71.44 - 89.30: 6 Dihedral angle restraints: 5314 sinusoidal: 2112 harmonic: 3202 Sorted by residual: dihedral pdb=" CA PRO E 722 " pdb=" C PRO E 722 " pdb=" N TRP E 723 " pdb=" CA TRP E 723 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLN C 434 " pdb=" C GLN C 434 " pdb=" N MET C 435 " pdb=" CA MET C 435 " ideal model delta harmonic sigma weight residual 180.00 163.93 16.07 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLN E 434 " pdb=" C GLN E 434 " pdb=" N MET E 435 " pdb=" CA MET E 435 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 926 0.034 - 0.068: 406 0.068 - 0.103: 125 0.103 - 0.137: 44 0.137 - 0.171: 3 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CB ILE E 487 " pdb=" CA ILE E 487 " pdb=" CG1 ILE E 487 " pdb=" CG2 ILE E 487 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" C2C PIO C1002 " pdb=" C1C PIO C1002 " pdb=" C3C PIO C1002 " pdb=" O2C PIO C1002 " both_signs ideal model delta sigma weight residual False -2.56 -2.40 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CB ILE C 487 " pdb=" CA ILE C 487 " pdb=" CG1 ILE C 487 " pdb=" CG2 ILE C 487 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO E 391 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO C 391 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 466 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO E 467 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 467 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 467 " -0.025 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 352 2.72 - 3.27: 9171 3.27 - 3.81: 15151 3.81 - 4.36: 18627 4.36 - 4.90: 31563 Nonbonded interactions: 74864 Sorted by model distance: nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.192 3.040 nonbonded pdb=" O PRO C 548 " pdb=" OH TYR C 553 " model vdw 2.268 3.040 nonbonded pdb=" NH2 ARG C 694 " pdb=" OD1 ASN C 736 " model vdw 2.291 3.120 nonbonded pdb=" O LEU C 863 " pdb=" OG1 THR C 866 " model vdw 2.317 3.040 ... (remaining 74859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.180 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 : 0.005 0.069 9162 Z= 0.209 Angle : 0.725 12.467 12474 Z= 0.334 Chirality : 0.043 0.171 1504 Planarity : 0.006 0.066 1494 Dihedral : 11.864 89.303 3250 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.95 % Allowed : 5.16 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1102 helix: 1.29 (0.18), residues: 750 sheet: None (None), residues: 0 loop : 0.21 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 388 TYR 0.015 0.002 TYR E 392 PHE 0.016 0.001 PHE E 471 TRP 0.015 0.002 TRP C 492 HIS 0.002 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 ( 9158) covalent geometry : angle 0.72462 / 0.33 (12462) hydrogen bonds : bond 0.14630 / 10.24 ( 576) hydrogen bonds : angle 5.07262 / 3.81 ( 1665) link_BETA1-4 : bond 0.00466 / 0.28 ( 2) link_BETA1-4 : angle 1.21327 / 0.70 ( 6) link_NAG-ASN : bond 0.00201 / 0.12 ( 2) link_NAG-ASN : angle 1.25788 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 219 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 426 LEU cc_start: 0.8879 (mt) cc_final: 0.8585 (mm) REVERT: C 472 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8223 (mm-30) REVERT: C 473 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: C 646 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.5948 (ppp80) REVERT: C 656 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.6883 (mtt180) REVERT: C 807 ASP cc_start: 0.8384 (m-30) cc_final: 0.8096 (m-30) REVERT: E 691 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7726 (mttm) REVERT: E 807 ASP cc_start: 0.8351 (m-30) cc_final: 0.8102 (m-30) outliers start: 9 outliers final: 2 residues processed: 223 average time/residue: 0.4961 time to fit residues: 118.2132 Evaluate side-chains 179 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 374 GLN C 377 GLN C 457 GLN C 482 ASN C 630 GLN C 651 HIS C 683 GLN E 377 GLN E 550 GLN E 630 GLN E 651 HIS E 683 GLN E 759 GLN E 819 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.128879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.106015 restraints weight = 10537.449| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.49 r_work: 0.2917 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9162 Z= 0.165 Angle : 0.551 6.712 12474 Z= 0.277 Chirality : 0.042 0.164 1504 Planarity : 0.006 0.059 1494 Dihedral : 8.055 79.314 1254 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.32 % Allowed : 10.84 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.25), residues: 1102 helix: 1.72 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.29 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 827 TYR 0.020 0.002 TYR C 824 PHE 0.019 0.001 PHE E 471 TRP 0.014 0.001 TRP C 492 HIS 0.002 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 9158) covalent geometry : angle 0.55033 / 0.28 (12462) hydrogen bonds : bond 0.04848 / 3.36 ( 576) hydrogen bonds : angle 4.27157 / 3.16 ( 1665) link_BETA1-4 : bond 0.00435 / 0.26 ( 2) link_BETA1-4 : angle 0.66725 / 0.37 ( 6) link_NAG-ASN : bond 0.00151 / 0.09 ( 2) link_NAG-ASN : angle 1.09598 / 0.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.338 Fit side-chains REVERT: C 384 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7643 (mtt180) REVERT: C 426 LEU cc_start: 0.8741 (mt) cc_final: 0.8482 (mm) REVERT: C 472 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8121 (mm-30) REVERT: C 473 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: C 592 LYS cc_start: 0.8444 (tttp) cc_final: 0.8026 (ttpp) REVERT: C 646 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.5386 (ppp80) REVERT: C 656 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.6626 (mtt180) REVERT: C 696 MET cc_start: 0.8746 (mmt) cc_final: 0.8424 (mmt) REVERT: C 807 ASP cc_start: 0.8191 (m-30) cc_final: 0.7735 (m-30) REVERT: E 399 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: E 429 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7807 (mm-30) REVERT: E 535 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8016 (mp0) REVERT: E 807 ASP cc_start: 0.8218 (m-30) cc_final: 0.7916 (m-30) REVERT: E 879 ARG cc_start: 0.7510 (mmp-170) cc_final: 0.6170 (mtt90) outliers start: 22 outliers final: 7 residues processed: 204 average time/residue: 0.4935 time to fit residues: 107.9068 Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN E 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.128768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.105952 restraints weight = 10466.490| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.48 r_work: 0.2919 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9162 Z= 0.151 Angle : 0.523 6.440 12474 Z= 0.262 Chirality : 0.041 0.161 1504 Planarity : 0.005 0.057 1494 Dihedral : 7.691 79.826 1251 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.95 % Allowed : 11.26 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.25), residues: 1102 helix: 1.83 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.28 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 827 TYR 0.016 0.002 TYR E 486 PHE 0.016 0.001 PHE E 471 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9158) covalent geometry : angle 0.52217 / 0.26 (12462) hydrogen bonds : bond 0.04468 / 3.10 ( 576) hydrogen bonds : angle 4.16807 / 3.08 ( 1665) link_BETA1-4 : bond 0.00459 / 0.28 ( 2) link_BETA1-4 : angle 0.73765 / 0.41 ( 6) link_NAG-ASN : bond 0.00154 / 0.10 ( 2) link_NAG-ASN : angle 1.13338 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7662 (mtt180) REVERT: C 394 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 426 LEU cc_start: 0.8742 (mt) cc_final: 0.8474 (mm) REVERT: C 472 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8130 (mm-30) REVERT: C 473 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: C 592 LYS cc_start: 0.8433 (tttp) cc_final: 0.8025 (ttpp) REVERT: C 646 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.5340 (ppp80) REVERT: C 656 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.6676 (mtt180) REVERT: C 705 ASP cc_start: 0.8571 (m-30) cc_final: 0.8348 (m-30) REVERT: C 807 ASP cc_start: 0.8194 (m-30) cc_final: 0.7758 (m-30) REVERT: E 429 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7722 (mm-30) REVERT: E 535 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7945 (mp0) REVERT: E 807 ASP cc_start: 0.8242 (m-30) cc_final: 0.7935 (m-30) REVERT: E 879 ARG cc_start: 0.7497 (mmp-170) cc_final: 0.6152 (mtt90) REVERT: E 887 ASP cc_start: 0.8344 (t0) cc_final: 0.8003 (t70) outliers start: 28 outliers final: 17 residues processed: 203 average time/residue: 0.4849 time to fit residues: 105.6533 Evaluate side-chains 205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 877 ILE Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 819 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.129030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.106225 restraints weight = 10539.897| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.48 r_work: 0.2922 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9162 Z= 0.146 Angle : 0.516 5.680 12474 Z= 0.258 Chirality : 0.041 0.161 1504 Planarity : 0.005 0.057 1494 Dihedral : 7.612 80.536 1251 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.05 % Allowed : 13.16 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1102 helix: 1.87 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.29 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 827 TYR 0.017 0.001 TYR C 824 PHE 0.017 0.001 PHE E 471 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9158) covalent geometry : angle 0.51541 / 0.26 (12462) hydrogen bonds : bond 0.04295 / 2.99 ( 576) hydrogen bonds : angle 4.12898 / 3.06 ( 1665) link_BETA1-4 : bond 0.00380 / 0.23 ( 2) link_BETA1-4 : angle 0.73233 / 0.41 ( 6) link_NAG-ASN : bond 0.00099 / 0.06 ( 2) link_NAG-ASN : angle 1.13954 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7683 (mtt180) REVERT: C 394 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8110 (mp) REVERT: C 426 LEU cc_start: 0.8756 (mt) cc_final: 0.8488 (mm) REVERT: C 472 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8140 (mm-30) REVERT: C 473 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: C 592 LYS cc_start: 0.8417 (tttp) cc_final: 0.7967 (ttpp) REVERT: C 646 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.5315 (ppp80) REVERT: C 656 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.6688 (mtt180) REVERT: C 807 ASP cc_start: 0.8213 (m-30) cc_final: 0.7874 (m-30) REVERT: C 844 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8178 (tt) REVERT: E 429 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7683 (mm-30) REVERT: E 535 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7911 (mp0) REVERT: E 592 LYS cc_start: 0.8601 (tttt) cc_final: 0.8078 (ttpt) REVERT: E 691 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7043 (mttm) REVERT: E 807 ASP cc_start: 0.8234 (m-30) cc_final: 0.7922 (m-30) REVERT: E 851 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7536 (ttpp) REVERT: E 879 ARG cc_start: 0.7519 (mmp-170) cc_final: 0.6192 (mtm-85) REVERT: E 887 ASP cc_start: 0.8326 (t0) cc_final: 0.8009 (t70) outliers start: 29 outliers final: 14 residues processed: 203 average time/residue: 0.4875 time to fit residues: 106.3285 Evaluate side-chains 204 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 851 LYS Chi-restraints excluded: chain E residue 864 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.126908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104172 restraints weight = 10552.876| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.46 r_work: 0.2894 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9162 Z= 0.199 Angle : 0.565 5.780 12474 Z= 0.281 Chirality : 0.043 0.162 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.673 81.962 1251 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.05 % Allowed : 13.68 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1102 helix: 1.70 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.19 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 603 TYR 0.016 0.002 TYR C 824 PHE 0.018 0.002 PHE E 471 TRP 0.013 0.002 TRP C 492 HIS 0.001 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 ( 9158) covalent geometry : angle 0.56411 / 0.28 (12462) hydrogen bonds : bond 0.04736 / 3.28 ( 576) hydrogen bonds : angle 4.23501 / 3.12 ( 1665) link_BETA1-4 : bond 0.00444 / 0.27 ( 2) link_BETA1-4 : angle 0.78277 / 0.44 ( 6) link_NAG-ASN : bond 0.00364 / 0.23 ( 2) link_NAG-ASN : angle 1.66956 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7664 (mtt180) REVERT: C 394 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 426 LEU cc_start: 0.8753 (mt) cc_final: 0.8485 (mm) REVERT: C 472 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8234 (mm-30) REVERT: C 473 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: C 592 LYS cc_start: 0.8439 (tttp) cc_final: 0.7990 (ttpp) REVERT: C 646 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.5872 (ppp80) REVERT: C 807 ASP cc_start: 0.8263 (m-30) cc_final: 0.7973 (m-30) REVERT: C 844 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8214 (tt) REVERT: E 390 TYR cc_start: 0.8661 (m-80) cc_final: 0.8432 (m-80) REVERT: E 399 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: E 429 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7706 (mm-30) REVERT: E 542 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8006 (tptp) REVERT: E 691 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7137 (mttm) REVERT: E 879 ARG cc_start: 0.7550 (mmp-170) cc_final: 0.6178 (mtt90) REVERT: E 887 ASP cc_start: 0.8386 (t0) cc_final: 0.8099 (t70) outliers start: 29 outliers final: 14 residues processed: 199 average time/residue: 0.5134 time to fit residues: 109.2712 Evaluate side-chains 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 542 LYS Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 864 ILE Chi-restraints excluded: chain E residue 881 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.108299 restraints weight = 10501.000| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.45 r_work: 0.2959 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9162 Z= 0.105 Angle : 0.479 5.584 12474 Z= 0.241 Chirality : 0.039 0.167 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.468 83.385 1251 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.00 % Allowed : 15.58 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1102 helix: 2.01 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.30 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 827 TYR 0.014 0.001 TYR E 486 PHE 0.016 0.001 PHE E 471 TRP 0.014 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9158) covalent geometry : angle 0.47789 / 0.24 (12462) hydrogen bonds : bond 0.03773 / 2.63 ( 576) hydrogen bonds : angle 4.06191 / 3.01 ( 1665) link_BETA1-4 : bond 0.00445 / 0.27 ( 2) link_BETA1-4 : angle 0.78367 / 0.42 ( 6) link_NAG-ASN : bond 0.00415 / 0.26 ( 2) link_NAG-ASN : angle 1.40027 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7670 (mtt180) REVERT: C 426 LEU cc_start: 0.8717 (mt) cc_final: 0.8468 (mm) REVERT: C 472 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8142 (mm-30) REVERT: C 473 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: C 592 LYS cc_start: 0.8369 (tttp) cc_final: 0.7943 (ttpp) REVERT: C 646 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.5411 (ppp80) REVERT: C 655 LEU cc_start: 0.8526 (mt) cc_final: 0.8293 (mm) REVERT: C 656 ARG cc_start: 0.7966 (mmt-90) cc_final: 0.6662 (mtt180) REVERT: C 807 ASP cc_start: 0.8196 (m-30) cc_final: 0.7893 (m-30) REVERT: C 835 LEU cc_start: 0.8762 (tp) cc_final: 0.8434 (tt) REVERT: E 429 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7625 (mm-30) REVERT: E 535 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7895 (mp0) REVERT: E 691 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7041 (mttm) REVERT: E 879 ARG cc_start: 0.7488 (mmp-170) cc_final: 0.6029 (mtm-85) REVERT: E 882 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8328 (mt-10) REVERT: E 887 ASP cc_start: 0.8242 (t0) cc_final: 0.7939 (t70) outliers start: 19 outliers final: 10 residues processed: 197 average time/residue: 0.4957 time to fit residues: 104.6033 Evaluate side-chains 198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 703 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.108223 restraints weight = 10500.917| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.46 r_work: 0.2951 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9162 Z= 0.115 Angle : 0.487 5.525 12474 Z= 0.244 Chirality : 0.040 0.150 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.382 83.600 1251 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.53 % Allowed : 15.89 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.25), residues: 1102 helix: 2.05 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.30 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 603 TYR 0.013 0.001 TYR C 824 PHE 0.016 0.001 PHE E 471 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9158) covalent geometry : angle 0.48442 / 0.24 (12462) hydrogen bonds : bond 0.03845 / 2.67 ( 576) hydrogen bonds : angle 4.04668 / 3.01 ( 1665) link_BETA1-4 : bond 0.00439 / 0.27 ( 2) link_BETA1-4 : angle 0.81229 / 0.43 ( 6) link_NAG-ASN : bond 0.00075 / 0.05 ( 2) link_NAG-ASN : angle 2.42320 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7634 (mtt180) REVERT: C 426 LEU cc_start: 0.8718 (mt) cc_final: 0.8479 (mm) REVERT: C 472 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8172 (mm-30) REVERT: C 473 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: C 592 LYS cc_start: 0.8387 (tttp) cc_final: 0.7966 (ttpp) REVERT: C 646 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.5369 (ppp80) REVERT: C 655 LEU cc_start: 0.8544 (mt) cc_final: 0.8316 (mm) REVERT: C 656 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.6692 (mtt180) REVERT: C 807 ASP cc_start: 0.8209 (m-30) cc_final: 0.7904 (m-30) REVERT: C 835 LEU cc_start: 0.8777 (tp) cc_final: 0.8453 (tt) REVERT: E 429 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7643 (mm-30) REVERT: E 535 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7904 (mp0) REVERT: E 646 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.5266 (ppp80) REVERT: E 879 ARG cc_start: 0.7476 (mmp-170) cc_final: 0.6016 (mtm-85) REVERT: E 882 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8330 (mt-10) REVERT: E 887 ASP cc_start: 0.8250 (t0) cc_final: 0.7969 (t70) outliers start: 24 outliers final: 14 residues processed: 204 average time/residue: 0.4792 time to fit residues: 104.9246 Evaluate side-chains 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.130169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.107619 restraints weight = 10389.107| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.46 r_work: 0.2947 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9162 Z= 0.124 Angle : 0.498 5.521 12474 Z= 0.250 Chirality : 0.040 0.151 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.338 84.358 1251 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.84 % Allowed : 15.68 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.25), residues: 1102 helix: 2.04 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.27 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 603 TYR 0.014 0.001 TYR C 824 PHE 0.016 0.001 PHE C 511 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 9158) covalent geometry : angle 0.49690 / 0.25 (12462) hydrogen bonds : bond 0.03884 / 2.69 ( 576) hydrogen bonds : angle 4.02540 / 2.98 ( 1665) link_BETA1-4 : bond 0.00334 / 0.20 ( 2) link_BETA1-4 : angle 0.75194 / 0.41 ( 6) link_NAG-ASN : bond 0.00055 / 0.03 ( 2) link_NAG-ASN : angle 1.70632 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7641 (mtt180) REVERT: C 426 LEU cc_start: 0.8715 (mt) cc_final: 0.8474 (mm) REVERT: C 472 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8175 (mm-30) REVERT: C 473 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: C 592 LYS cc_start: 0.8393 (tttp) cc_final: 0.7972 (ttpp) REVERT: C 646 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.5343 (ppp80) REVERT: C 655 LEU cc_start: 0.8534 (mt) cc_final: 0.8304 (mm) REVERT: C 656 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.6705 (mtt180) REVERT: C 807 ASP cc_start: 0.8202 (m-30) cc_final: 0.7939 (m-30) REVERT: C 835 LEU cc_start: 0.8795 (tp) cc_final: 0.8476 (tt) REVERT: E 399 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: E 429 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7642 (mm-30) REVERT: E 535 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7891 (mp0) REVERT: E 646 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.5255 (ppp80) REVERT: E 807 ASP cc_start: 0.8218 (m-30) cc_final: 0.7927 (m-30) REVERT: E 879 ARG cc_start: 0.7474 (mmp-170) cc_final: 0.6130 (mtm-85) REVERT: E 887 ASP cc_start: 0.8254 (t0) cc_final: 0.7997 (t70) outliers start: 27 outliers final: 15 residues processed: 202 average time/residue: 0.4911 time to fit residues: 106.6090 Evaluate side-chains 205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.130241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.107681 restraints weight = 10487.116| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.46 r_work: 0.2944 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9162 Z= 0.125 Angle : 0.509 8.012 12474 Z= 0.253 Chirality : 0.040 0.150 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.329 85.207 1251 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.21 % Allowed : 16.63 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.25), residues: 1102 helix: 2.04 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.30 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 603 TYR 0.014 0.001 TYR C 824 PHE 0.016 0.001 PHE C 511 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 9158) covalent geometry : angle 0.50785 / 0.25 (12462) hydrogen bonds : bond 0.03894 / 2.70 ( 576) hydrogen bonds : angle 4.02273 / 2.98 ( 1665) link_BETA1-4 : bond 0.00325 / 0.20 ( 2) link_BETA1-4 : angle 0.73045 / 0.40 ( 6) link_NAG-ASN : bond 0.00089 / 0.05 ( 2) link_NAG-ASN : angle 1.51335 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7665 (mtt180) REVERT: C 426 LEU cc_start: 0.8715 (mt) cc_final: 0.8471 (mm) REVERT: C 472 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 473 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7374 (tt0) REVERT: C 592 LYS cc_start: 0.8390 (tttp) cc_final: 0.7971 (ttpp) REVERT: C 646 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.5338 (ppp80) REVERT: C 655 LEU cc_start: 0.8533 (mt) cc_final: 0.8300 (mm) REVERT: C 656 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.6720 (mtt180) REVERT: C 807 ASP cc_start: 0.8204 (m-30) cc_final: 0.7905 (m-30) REVERT: C 835 LEU cc_start: 0.8801 (tp) cc_final: 0.8484 (tt) REVERT: E 399 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: E 429 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7628 (mm-30) REVERT: E 646 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.5288 (ppp80) REVERT: E 807 ASP cc_start: 0.8230 (m-30) cc_final: 0.7914 (m-30) REVERT: E 882 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8383 (mt-10) REVERT: E 887 ASP cc_start: 0.8258 (t0) cc_final: 0.8000 (t70) outliers start: 21 outliers final: 13 residues processed: 198 average time/residue: 0.4687 time to fit residues: 99.8721 Evaluate side-chains 198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.130617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.107688 restraints weight = 10483.690| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.54 r_work: 0.2940 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9162 Z= 0.119 Angle : 0.498 5.722 12474 Z= 0.251 Chirality : 0.040 0.149 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.096 86.371 1248 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.79 % Allowed : 17.05 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.25), residues: 1102 helix: 2.05 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.31 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 603 TYR 0.015 0.001 TYR C 824 PHE 0.017 0.001 PHE C 511 TRP 0.013 0.001 TRP C 492 HIS 0.001 0.000 HIS C 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9158) covalent geometry : angle 0.49737 / 0.25 (12462) hydrogen bonds : bond 0.03841 / 2.66 ( 576) hydrogen bonds : angle 4.00487 / 2.97 ( 1665) link_BETA1-4 : bond 0.00307 / 0.19 ( 2) link_BETA1-4 : angle 0.74917 / 0.41 ( 6) link_NAG-ASN : bond 0.00070 / 0.04 ( 2) link_NAG-ASN : angle 1.36563 / 0.80 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7672 (mtt180) REVERT: C 426 LEU cc_start: 0.8712 (mt) cc_final: 0.8472 (mm) REVERT: C 472 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8193 (mm-30) REVERT: C 473 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7390 (tt0) REVERT: C 592 LYS cc_start: 0.8388 (tttp) cc_final: 0.7968 (ttpp) REVERT: C 646 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.5339 (ppp80) REVERT: C 655 LEU cc_start: 0.8535 (mt) cc_final: 0.8301 (mm) REVERT: C 656 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.6716 (mtt180) REVERT: C 807 ASP cc_start: 0.8223 (m-30) cc_final: 0.7925 (m-30) REVERT: C 835 LEU cc_start: 0.8801 (tp) cc_final: 0.8464 (tt) REVERT: E 399 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: E 535 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7935 (mp0) REVERT: E 646 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.5275 (ppp80) REVERT: E 691 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7571 (ttmm) REVERT: E 807 ASP cc_start: 0.8255 (m-30) cc_final: 0.7942 (m-30) REVERT: E 882 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8380 (mt-10) REVERT: E 887 ASP cc_start: 0.8250 (t0) cc_final: 0.7973 (t70) outliers start: 17 outliers final: 13 residues processed: 197 average time/residue: 0.4854 time to fit residues: 102.4607 Evaluate side-chains 202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 881 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 484 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 644 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 673 LEU Chi-restraints excluded: chain E residue 727 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 0.0870 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.131349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.108963 restraints weight = 10360.796| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.45 r_work: 0.2966 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9162 Z= 0.110 Angle : 0.500 8.499 12474 Z= 0.250 Chirality : 0.040 0.148 1504 Planarity : 0.005 0.055 1494 Dihedral : 7.063 87.314 1248 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.11 % Allowed : 16.95 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.25), residues: 1102 helix: 2.10 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.33 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 603 TYR 0.014 0.001 TYR C 824 PHE 0.017 0.001 PHE C 511 TRP 0.013 0.001 TRP C 492 HIS 0.002 0.000 HIS E 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9158) covalent geometry : angle 0.49971 / 0.25 (12462) hydrogen bonds : bond 0.03710 / 2.57 ( 576) hydrogen bonds : angle 3.97476 / 2.95 ( 1665) link_BETA1-4 : bond 0.00323 / 0.20 ( 2) link_BETA1-4 : angle 0.74970 / 0.41 ( 6) link_NAG-ASN : bond 0.00091 / 0.06 ( 2) link_NAG-ASN : angle 1.23026 / 0.72 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4519.70 seconds wall clock time: 77 minutes 27.09 seconds (4647.09 seconds total)