Starting phenix.real_space_refine on Wed Sep 17 04:45:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ziw_60131/09_2025/8ziw_60131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ziw_60131/09_2025/8ziw_60131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ziw_60131/09_2025/8ziw_60131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ziw_60131/09_2025/8ziw_60131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ziw_60131/09_2025/8ziw_60131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ziw_60131/09_2025/8ziw_60131.map" } resolution = 2.92 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= 0.030 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2778 2.51 5 N 711 2.21 5 O 931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4450 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2181 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 261} Chain: "D" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1835 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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 Time building chain proxies: 1.34, per 1000 atoms: 0.30 Number of scatterers: 4450 At special positions: 0 Unit cell: (79.872, 96.512, 131.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 931 8.00 N 711 7.00 C 2778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS D 896 " distance=2.03 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 826 " distance=2.03 Simple disulfide: pdb=" SG CYS D 910 " - pdb=" SG CYS D 977 " distance=2.03 Simple disulfide: pdb=" SG CYS D 941 " - pdb=" SG CYS D 956 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA B 3 " - " MAN B 4 " " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " BETA1-6 " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG B 1 " - " ASN A 534 " " NAG C 1 " - " ASN A 630 " " NAG E 1 " - " ASN A 682 " " NAG F 1 " - " ASN A 706 " " NAG G 1 " - " ASN A 725 " " NAG H 1 " - " ASN D 848 " " NAG I 1 " - " ASN D 887 " " NAG J 1 " - " ASN D 909 " " NAG K 1 " - " ASN D 949 " " NAG L 1 " - " ASN D 980 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 158.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'D' and resid 833 through 835 No H-bonds generated for 'chain 'D' and resid 833 through 835' Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.579A pdb=" N GLN D 943 " --> pdb=" O GLU D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 952 No H-bonds generated for 'chain 'D' and resid 950 through 952' Processing helix chain 'D' and resid 1010 through 1017 removed outlier: 4.133A pdb=" N PHE D1017 " --> pdb=" O TRP D1013 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 538 removed outlier: 4.161A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 570 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.608A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.629A pdb=" N ARG A 692 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.629A pdb=" N ARG A 692 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.805A pdb=" N ASN A 742 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 750 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 789 through 790 removed outlier: 4.121A pdb=" N CYS D 956 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 957 " --> pdb=" O GLY D1002 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D1002 " --> pdb=" O ALA D 957 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D1003 " --> pdb=" O SER D 990 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 988 " --> pdb=" O ALA D1005 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU D 985 " --> pdb=" O CYS D 977 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS D 977 " --> pdb=" O LEU D 985 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA D 913 " --> pdb=" O PRO D 974 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 799 through 804 removed outlier: 3.862A pdb=" N CYS D 810 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 804 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU D 808 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 855 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TRP D 837 " --> pdb=" O ILE D 859 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1382 1.34 - 1.46: 1098 1.46 - 1.58: 2037 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 4554 Sorted by residual: bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C5 MAN H 4 " pdb=" O5 MAN H 4 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 MAN I 4 " pdb=" C2 MAN I 4 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C GLU A 532 " pdb=" N PRO A 533 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.42e+00 ... (remaining 4549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 5838 1.37 - 2.74: 238 2.74 - 4.11: 65 4.11 - 5.48: 51 5.48 - 6.85: 18 Bond angle restraints: 6210 Sorted by residual: angle pdb=" N ARG D 982 " pdb=" CA ARG D 982 " pdb=" C ARG D 982 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N LEU D 849 " pdb=" CA LEU D 849 " pdb=" C LEU D 849 " ideal model delta sigma weight residual 113.43 110.25 3.18 1.26e+00 6.30e-01 6.37e+00 angle pdb=" C THR A 522 " pdb=" CA THR A 522 " pdb=" CB THR A 522 " ideal model delta sigma weight residual 110.42 115.41 -4.99 1.99e+00 2.53e-01 6.30e+00 angle pdb=" CA ARG D 982 " pdb=" C ARG D 982 " pdb=" N TRP D 983 " ideal model delta sigma weight residual 119.26 116.48 2.78 1.14e+00 7.69e-01 5.96e+00 angle pdb=" C3 NAG I 2 " pdb=" C4 NAG I 2 " pdb=" O4 NAG I 2 " ideal model delta sigma weight residual 107.29 114.14 -6.85 3.00e+00 1.11e-01 5.21e+00 ... (remaining 6205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 2951 23.74 - 47.48: 63 47.48 - 71.22: 30 71.22 - 94.96: 55 94.96 - 118.70: 41 Dihedral angle restraints: 3140 sinusoidal: 1660 harmonic: 1480 Sorted by residual: dihedral pdb=" CB CYS A 772 " pdb=" SG CYS A 772 " pdb=" SG CYS D 896 " pdb=" CB CYS D 896 " ideal model delta sinusoidal sigma weight residual -86.00 -123.99 37.99 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" C2 MAN H 4 " pdb=" C1 MAN H 4 " pdb=" O5 MAN H 4 " pdb=" C5 MAN H 4 " ideal model delta sinusoidal sigma weight residual -57.62 61.08 -118.70 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.29 110.42 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 676 0.080 - 0.160: 92 0.160 - 0.240: 2 0.240 - 0.319: 11 0.319 - 0.399: 2 Chirality restraints: 783 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 909 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 534 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 780 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 731 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 732 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 542 " -0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 543 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 973 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO D 974 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 974 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 974 " -0.015 5.00e-02 4.00e+02 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 818 2.78 - 3.31: 4012 3.31 - 3.84: 6956 3.84 - 4.37: 7702 4.37 - 4.90: 13175 Nonbonded interactions: 32663 Sorted by model distance: nonbonded pdb=" O3 NAG I 2 " pdb=" O6 MAN I 4 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASN D 875 " pdb=" ND2 ASN D 953 " model vdw 2.263 3.120 nonbonded pdb=" NE1 TRP A 707 " pdb=" OG SER A 712 " model vdw 2.336 3.120 nonbonded pdb=" OD1 ASP D 874 " pdb=" ND2 ASN D 953 " model vdw 2.342 3.120 nonbonded pdb=" O TRP D1013 " pdb=" OG SER D1016 " model vdw 2.362 3.040 ... (remaining 32658 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 'B' selection = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5793 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 0.048 4593 Z= 0.243 Angle : 0.883 9.468 6322 Z= 0.351 Chirality : 0.060 0.399 783 Planarity : 0.003 0.030 766 Dihedral : 22.014 118.698 2177 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.81 % Allowed : 3.84 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.82 (0.38), residues: 515 helix: 0.01 (0.95), residues: 35 sheet: 1.00 (0.51), residues: 113 loop : -1.19 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1009 TYR 0.005 0.001 TYR A 546 PHE 0.004 0.001 PHE A 693 TRP 0.004 0.000 TRP A 554 HIS 0.003 0.000 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4554) covalent geometry : angle 0.82232 ( 6210) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.39626 ( 10) hydrogen bonds : bond 0.27402 ( 78) hydrogen bonds : angle 11.62711 ( 222) link_ALPHA1-3 : bond 0.00668 ( 2) link_ALPHA1-3 : angle 1.40351 ( 6) link_ALPHA1-6 : bond 0.00820 ( 2) link_ALPHA1-6 : angle 1.77729 ( 6) link_BETA1-4 : bond 0.00563 ( 18) link_BETA1-4 : angle 3.10784 ( 54) link_BETA1-6 : bond 0.00654 ( 2) link_BETA1-6 : angle 1.41513 ( 6) link_NAG-ASN : bond 0.00434 ( 10) link_NAG-ASN : angle 2.31909 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 LEU cc_start: 0.8380 (mt) cc_final: 0.8161 (mp) outliers start: 8 outliers final: 2 residues processed: 81 average time/residue: 0.3648 time to fit residues: 31.1887 Evaluate side-chains 73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 853 GLN D 881 HIS ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 968 GLN ** D 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.205586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.191406 restraints weight = 8211.167| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 3.34 r_work: 0.4373 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4593 Z= 0.164 Angle : 0.884 9.174 6322 Z= 0.371 Chirality : 0.054 0.338 783 Planarity : 0.005 0.040 766 Dihedral : 18.328 101.447 1242 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 2.48 % Allowed : 9.71 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.06 (0.37), residues: 515 helix: -0.69 (0.91), residues: 33 sheet: 0.60 (0.50), residues: 116 loop : -1.23 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 694 TYR 0.016 0.002 TYR D 948 PHE 0.016 0.002 PHE D1010 TRP 0.009 0.002 TRP D 819 HIS 0.008 0.002 HIS D 881 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4554) covalent geometry : angle 0.79466 ( 6210) SS BOND : bond 0.00420 ( 5) SS BOND : angle 0.61145 ( 10) hydrogen bonds : bond 0.04811 ( 78) hydrogen bonds : angle 8.70834 ( 222) link_ALPHA1-3 : bond 0.00960 ( 2) link_ALPHA1-3 : angle 2.40794 ( 6) link_ALPHA1-6 : bond 0.01149 ( 2) link_ALPHA1-6 : angle 2.85533 ( 6) link_BETA1-4 : bond 0.00605 ( 18) link_BETA1-4 : angle 3.59922 ( 54) link_BETA1-6 : bond 0.00718 ( 2) link_BETA1-6 : angle 2.76382 ( 6) link_NAG-ASN : bond 0.00705 ( 10) link_NAG-ASN : angle 2.46845 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 880 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6413 (mtp) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.4122 time to fit residues: 32.3620 Evaluate side-chains 74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.200096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.185580 restraints weight = 7960.427| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 3.35 r_work: 0.4302 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4593 Z= 0.227 Angle : 0.975 9.704 6322 Z= 0.413 Chirality : 0.058 0.341 783 Planarity : 0.005 0.036 766 Dihedral : 15.128 95.089 1241 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 2.93 % Allowed : 11.74 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.65 (0.36), residues: 515 helix: -1.73 (0.71), residues: 34 sheet: -0.11 (0.48), residues: 117 loop : -1.45 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 624 TYR 0.018 0.002 TYR D 948 PHE 0.011 0.002 PHE D1010 TRP 0.012 0.002 TRP D 983 HIS 0.009 0.002 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 4554) covalent geometry : angle 0.87586 ( 6210) SS BOND : bond 0.00573 ( 5) SS BOND : angle 0.72374 ( 10) hydrogen bonds : bond 0.04386 ( 78) hydrogen bonds : angle 8.18766 ( 222) link_ALPHA1-3 : bond 0.01197 ( 2) link_ALPHA1-3 : angle 1.47764 ( 6) link_ALPHA1-6 : bond 0.01059 ( 2) link_ALPHA1-6 : angle 3.09539 ( 6) link_BETA1-4 : bond 0.00716 ( 18) link_BETA1-4 : angle 3.98528 ( 54) link_BETA1-6 : bond 0.00518 ( 2) link_BETA1-6 : angle 2.59289 ( 6) link_NAG-ASN : bond 0.00905 ( 10) link_NAG-ASN : angle 3.01528 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 LEU cc_start: 0.8430 (mt) cc_final: 0.8179 (mp) outliers start: 13 outliers final: 6 residues processed: 94 average time/residue: 0.3156 time to fit residues: 31.5261 Evaluate side-chains 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 14 optimal weight: 0.0770 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN D 902 GLN D 938 ASN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.204459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.190059 restraints weight = 7935.645| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 3.35 r_work: 0.4354 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4593 Z= 0.131 Angle : 0.866 9.427 6322 Z= 0.360 Chirality : 0.052 0.304 783 Planarity : 0.005 0.061 766 Dihedral : 12.244 88.510 1241 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.71 % Allowed : 14.00 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.58 (0.35), residues: 515 helix: -1.53 (0.79), residues: 33 sheet: -0.06 (0.48), residues: 110 loop : -1.40 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 908 TYR 0.012 0.001 TYR D 948 PHE 0.019 0.002 PHE A 551 TRP 0.018 0.002 TRP D 983 HIS 0.005 0.001 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4554) covalent geometry : angle 0.78399 ( 6210) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.61533 ( 10) hydrogen bonds : bond 0.03463 ( 78) hydrogen bonds : angle 7.56814 ( 222) link_ALPHA1-3 : bond 0.01174 ( 2) link_ALPHA1-3 : angle 1.88659 ( 6) link_ALPHA1-6 : bond 0.01259 ( 2) link_ALPHA1-6 : angle 3.22214 ( 6) link_BETA1-4 : bond 0.00569 ( 18) link_BETA1-4 : angle 3.42524 ( 54) link_BETA1-6 : bond 0.00747 ( 2) link_BETA1-6 : angle 2.05461 ( 6) link_NAG-ASN : bond 0.00648 ( 10) link_NAG-ASN : angle 2.40032 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7650 (ptp90) REVERT: D 880 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6224 (mtp) outliers start: 12 outliers final: 7 residues processed: 79 average time/residue: 0.4178 time to fit residues: 34.6891 Evaluate side-chains 80 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 814 LEU Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 ASN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.198921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.184747 restraints weight = 7925.837| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 3.15 r_work: 0.4293 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4593 Z= 0.234 Angle : 0.977 10.662 6322 Z= 0.417 Chirality : 0.058 0.335 783 Planarity : 0.006 0.054 766 Dihedral : 12.607 88.553 1241 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 3.39 % Allowed : 13.54 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.98 (0.35), residues: 515 helix: -1.84 (0.72), residues: 34 sheet: -0.16 (0.48), residues: 112 loop : -1.76 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 624 TYR 0.016 0.002 TYR D 959 PHE 0.023 0.002 PHE A 551 TRP 0.017 0.003 TRP D 983 HIS 0.007 0.002 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 4554) covalent geometry : angle 0.87853 ( 6210) SS BOND : bond 0.00506 ( 5) SS BOND : angle 0.86608 ( 10) hydrogen bonds : bond 0.03447 ( 78) hydrogen bonds : angle 7.74541 ( 222) link_ALPHA1-3 : bond 0.01321 ( 2) link_ALPHA1-3 : angle 1.67197 ( 6) link_ALPHA1-6 : bond 0.01225 ( 2) link_ALPHA1-6 : angle 3.25468 ( 6) link_BETA1-4 : bond 0.00765 ( 18) link_BETA1-4 : angle 3.90971 ( 54) link_BETA1-6 : bond 0.00425 ( 2) link_BETA1-6 : angle 2.53316 ( 6) link_NAG-ASN : bond 0.00864 ( 10) link_NAG-ASN : angle 3.11192 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 LEU cc_start: 0.8390 (mt) cc_final: 0.8167 (mp) outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 0.3252 time to fit residues: 31.4551 Evaluate side-chains 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 814 LEU Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 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 = 0.4552 r_free = 0.4552 target = 0.200146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.185590 restraints weight = 8065.094| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 3.27 r_work: 0.4303 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4593 Z= 0.171 Angle : 0.912 9.958 6322 Z= 0.386 Chirality : 0.055 0.293 783 Planarity : 0.006 0.055 766 Dihedral : 11.905 81.538 1241 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 2.71 % Allowed : 15.35 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.11 (0.35), residues: 515 helix: -1.93 (0.71), residues: 33 sheet: -0.35 (0.48), residues: 112 loop : -1.82 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 692 TYR 0.013 0.002 TYR D 948 PHE 0.021 0.002 PHE A 551 TRP 0.016 0.002 TRP D 983 HIS 0.006 0.001 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4554) covalent geometry : angle 0.82301 ( 6210) SS BOND : bond 0.00300 ( 5) SS BOND : angle 0.72860 ( 10) hydrogen bonds : bond 0.03391 ( 78) hydrogen bonds : angle 7.49544 ( 222) link_ALPHA1-3 : bond 0.01270 ( 2) link_ALPHA1-3 : angle 1.63409 ( 6) link_ALPHA1-6 : bond 0.01348 ( 2) link_ALPHA1-6 : angle 3.25659 ( 6) link_BETA1-4 : bond 0.00671 ( 18) link_BETA1-4 : angle 3.67239 ( 54) link_BETA1-6 : bond 0.00623 ( 2) link_BETA1-6 : angle 2.03185 ( 6) link_NAG-ASN : bond 0.00672 ( 10) link_NAG-ASN : angle 2.70306 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8207 (tm-30) REVERT: A 679 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7615 (ptp90) REVERT: A 742 ASN cc_start: 0.6359 (t0) cc_final: 0.6127 (t0) outliers start: 12 outliers final: 6 residues processed: 88 average time/residue: 0.3422 time to fit residues: 31.9475 Evaluate side-chains 90 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 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 = 0.4549 r_free = 0.4549 target = 0.199865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.185389 restraints weight = 7925.514| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 3.23 r_work: 0.4302 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4593 Z= 0.167 Angle : 0.909 10.305 6322 Z= 0.381 Chirality : 0.055 0.298 783 Planarity : 0.006 0.061 766 Dihedral : 11.418 68.511 1241 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 4.06 % Allowed : 14.45 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.20 (0.35), residues: 515 helix: -1.80 (0.73), residues: 33 sheet: -0.42 (0.48), residues: 112 loop : -1.90 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 692 TYR 0.013 0.001 TYR D 959 PHE 0.018 0.001 PHE A 551 TRP 0.018 0.002 TRP D 983 HIS 0.006 0.001 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4554) covalent geometry : angle 0.81926 ( 6210) SS BOND : bond 0.00684 ( 5) SS BOND : angle 0.68888 ( 10) hydrogen bonds : bond 0.03063 ( 78) hydrogen bonds : angle 7.25367 ( 222) link_ALPHA1-3 : bond 0.01297 ( 2) link_ALPHA1-3 : angle 1.67474 ( 6) link_ALPHA1-6 : bond 0.01422 ( 2) link_ALPHA1-6 : angle 3.24546 ( 6) link_BETA1-4 : bond 0.00691 ( 18) link_BETA1-4 : angle 3.67138 ( 54) link_BETA1-6 : bond 0.00612 ( 2) link_BETA1-6 : angle 2.07737 ( 6) link_NAG-ASN : bond 0.00712 ( 10) link_NAG-ASN : angle 2.72188 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 742 ASN cc_start: 0.6595 (t0) cc_final: 0.6356 (t0) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.3302 time to fit residues: 33.3559 Evaluate side-chains 93 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 36 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 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 = 0.4560 r_free = 0.4560 target = 0.200987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.186238 restraints weight = 7917.792| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 3.40 r_work: 0.4305 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4593 Z= 0.140 Angle : 0.892 9.305 6322 Z= 0.375 Chirality : 0.052 0.304 783 Planarity : 0.005 0.059 766 Dihedral : 10.552 59.750 1241 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.71 % Allowed : 16.25 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.14 (0.36), residues: 515 helix: -1.75 (0.74), residues: 33 sheet: -0.54 (0.49), residues: 107 loop : -1.78 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 692 TYR 0.010 0.001 TYR D 948 PHE 0.027 0.002 PHE A 551 TRP 0.013 0.002 TRP D 915 HIS 0.007 0.001 HIS D 844 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4554) covalent geometry : angle 0.81349 ( 6210) SS BOND : bond 0.00338 ( 5) SS BOND : angle 0.70119 ( 10) hydrogen bonds : bond 0.03161 ( 78) hydrogen bonds : angle 7.01844 ( 222) link_ALPHA1-3 : bond 0.01190 ( 2) link_ALPHA1-3 : angle 1.56969 ( 6) link_ALPHA1-6 : bond 0.01474 ( 2) link_ALPHA1-6 : angle 2.96514 ( 6) link_BETA1-4 : bond 0.00632 ( 18) link_BETA1-4 : angle 3.44630 ( 54) link_BETA1-6 : bond 0.00710 ( 2) link_BETA1-6 : angle 1.76366 ( 6) link_NAG-ASN : bond 0.00632 ( 10) link_NAG-ASN : angle 2.47128 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 679 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7612 (ptp90) REVERT: A 742 ASN cc_start: 0.6623 (t0) cc_final: 0.6376 (t0) REVERT: D 880 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6235 (mtp) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.3398 time to fit residues: 28.1953 Evaluate side-chains 81 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 820 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 29 optimal weight: 0.2980 chunk 27 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 944 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 = 0.4561 r_free = 0.4561 target = 0.201407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.186736 restraints weight = 7905.668| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 3.36 r_work: 0.4310 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4593 Z= 0.137 Angle : 0.873 11.485 6322 Z= 0.368 Chirality : 0.052 0.301 783 Planarity : 0.005 0.060 766 Dihedral : 10.178 59.820 1241 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 2.48 % Allowed : 16.48 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.15 (0.36), residues: 515 helix: -1.69 (0.72), residues: 33 sheet: -0.55 (0.49), residues: 107 loop : -1.80 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 692 TYR 0.012 0.001 TYR A 596 PHE 0.029 0.002 PHE A 551 TRP 0.023 0.002 TRP D 915 HIS 0.006 0.001 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4554) covalent geometry : angle 0.79542 ( 6210) SS BOND : bond 0.00322 ( 5) SS BOND : angle 0.77100 ( 10) hydrogen bonds : bond 0.02949 ( 78) hydrogen bonds : angle 6.83721 ( 222) link_ALPHA1-3 : bond 0.01157 ( 2) link_ALPHA1-3 : angle 1.51104 ( 6) link_ALPHA1-6 : bond 0.01422 ( 2) link_ALPHA1-6 : angle 2.66761 ( 6) link_BETA1-4 : bond 0.00638 ( 18) link_BETA1-4 : angle 3.40425 ( 54) link_BETA1-6 : bond 0.00694 ( 2) link_BETA1-6 : angle 1.78295 ( 6) link_NAG-ASN : bond 0.00606 ( 10) link_NAG-ASN : angle 2.47140 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 679 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7714 (ptp90) REVERT: A 742 ASN cc_start: 0.6603 (t0) cc_final: 0.6349 (t0) REVERT: D 880 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6258 (mtp) REVERT: D 915 TRP cc_start: 0.7997 (m-90) cc_final: 0.7709 (m-90) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.3579 time to fit residues: 27.6799 Evaluate side-chains 75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 945 MET Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 0.0370 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.198586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.184437 restraints weight = 7768.647| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 3.14 r_work: 0.4287 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4593 Z= 0.183 Angle : 0.943 11.513 6322 Z= 0.402 Chirality : 0.056 0.305 783 Planarity : 0.005 0.062 766 Dihedral : 10.668 58.497 1241 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 2.71 % Allowed : 17.16 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.29 (0.36), residues: 515 helix: -1.73 (0.73), residues: 33 sheet: -0.45 (0.50), residues: 112 loop : -1.99 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 692 TYR 0.012 0.002 TYR D 948 PHE 0.030 0.002 PHE A 551 TRP 0.019 0.002 TRP A 554 HIS 0.006 0.001 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4554) covalent geometry : angle 0.85629 ( 6210) SS BOND : bond 0.00395 ( 5) SS BOND : angle 1.02550 ( 10) hydrogen bonds : bond 0.03099 ( 78) hydrogen bonds : angle 7.05043 ( 222) link_ALPHA1-3 : bond 0.01205 ( 2) link_ALPHA1-3 : angle 1.36621 ( 6) link_ALPHA1-6 : bond 0.01300 ( 2) link_ALPHA1-6 : angle 2.50604 ( 6) link_BETA1-4 : bond 0.00780 ( 18) link_BETA1-4 : angle 3.71296 ( 54) link_BETA1-6 : bond 0.00586 ( 2) link_BETA1-6 : angle 2.22662 ( 6) link_NAG-ASN : bond 0.00734 ( 10) link_NAG-ASN : angle 2.83292 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 742 ASN cc_start: 0.6844 (t0) cc_final: 0.6606 (t0) REVERT: D 880 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6205 (mtp) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.3211 time to fit residues: 27.6318 Evaluate side-chains 82 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 980 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** D 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.198463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.184433 restraints weight = 7748.170| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.17 r_work: 0.4291 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4593 Z= 0.171 Angle : 0.925 11.526 6322 Z= 0.394 Chirality : 0.055 0.312 783 Planarity : 0.005 0.063 766 Dihedral : 10.509 59.507 1241 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 1.81 % Allowed : 18.51 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.35 (0.36), residues: 515 helix: -1.69 (0.73), residues: 33 sheet: -0.49 (0.50), residues: 112 loop : -2.04 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 692 TYR 0.013 0.002 TYR A 596 PHE 0.029 0.002 PHE A 551 TRP 0.023 0.002 TRP D 915 HIS 0.006 0.001 HIS D1019 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4554) covalent geometry : angle 0.84015 ( 6210) SS BOND : bond 0.00277 ( 5) SS BOND : angle 1.04688 ( 10) hydrogen bonds : bond 0.02977 ( 78) hydrogen bonds : angle 6.97187 ( 222) link_ALPHA1-3 : bond 0.01167 ( 2) link_ALPHA1-3 : angle 1.39701 ( 6) link_ALPHA1-6 : bond 0.01243 ( 2) link_ALPHA1-6 : angle 2.50197 ( 6) link_BETA1-4 : bond 0.00757 ( 18) link_BETA1-4 : angle 3.65853 ( 54) link_BETA1-6 : bond 0.00630 ( 2) link_BETA1-6 : angle 2.10233 ( 6) link_NAG-ASN : bond 0.00662 ( 10) link_NAG-ASN : angle 2.67738 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.83 seconds wall clock time: 30 minutes 35.19 seconds (1835.19 seconds total)