Starting phenix.real_space_refine on Wed Feb 4 11:13:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7g_39813/02_2026/8z7g_39813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7g_39813/02_2026/8z7g_39813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2026/8z7g_39813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2026/8z7g_39813.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2026/8z7g_39813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2026/8z7g_39813.cif" } resolution = 3.06 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= -0.050 sd= 0.275 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 51 5.16 5 C 6552 2.51 5 N 1719 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10362 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3370 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3370 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3370 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.84, per 1000 atoms: 0.27 Number of scatterers: 10362 At special positions: 0 Unit cell: (76.424, 77.356, 272.144, 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 51 16.00 O 2040 8.00 N 1719 7.00 C 6552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 709 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 525.3 milliseconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 45.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.524A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 769 Processing helix chain 'A' and resid 835 through 842 removed outlier: 3.686A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.748A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 894 No H-bonds generated for 'chain 'A' and resid 892 through 894' Processing helix chain 'A' and resid 895 through 1033 removed outlier: 3.828A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.544A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 769 removed outlier: 3.525A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 842 removed outlier: 3.702A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.756A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 894 No H-bonds generated for 'chain 'B' and resid 892 through 894' Processing helix chain 'B' and resid 895 through 1033 removed outlier: 3.836A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.524A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 842 removed outlier: 3.705A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.756A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 894 No H-bonds generated for 'chain 'C' and resid 892 through 894' Processing helix chain 'C' and resid 895 through 1033 removed outlier: 3.825A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 727 removed outlier: 7.270A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AA3, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AA4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 727 removed outlier: 7.303A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AA7, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AA8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 727 removed outlier: 7.231A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB2, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AB3, first strand: chain 'C' and resid 1094 through 1097 584 hydrogen bonds defined for protein. 1716 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: 1.57 Time building geometry restraints manager: 1.31 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: 3390 1.34 - 1.46: 2299 1.46 - 1.58: 4784 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 10545 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 10540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 13964 1.07 - 2.13: 289 2.13 - 3.20: 87 3.20 - 4.26: 6 4.26 - 5.33: 3 Bond angle restraints: 14349 Sorted by residual: angle pdb=" C GLY B 832 " pdb=" N PHE B 833 " pdb=" CA PHE B 833 " ideal model delta sigma weight residual 121.54 125.25 -3.71 1.91e+00 2.74e-01 3.76e+00 angle pdb=" C GLY C 832 " pdb=" N PHE C 833 " pdb=" CA PHE C 833 " ideal model delta sigma weight residual 121.54 125.22 -3.68 1.91e+00 2.74e-01 3.71e+00 angle pdb=" C GLY A 832 " pdb=" N PHE A 833 " pdb=" CA PHE A 833 " ideal model delta sigma weight residual 121.54 125.20 -3.66 1.91e+00 2.74e-01 3.67e+00 angle pdb=" N PRO B 793 " pdb=" CA PRO B 793 " pdb=" C PRO B 793 " ideal model delta sigma weight residual 110.50 113.17 -2.67 1.57e+00 4.06e-01 2.89e+00 angle pdb=" C SER B 708 " pdb=" N ASN B 709 " pdb=" CA ASN B 709 " ideal model delta sigma weight residual 122.82 124.91 -2.09 1.42e+00 4.96e-01 2.16e+00 ... (remaining 14344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 6080 11.17 - 22.34: 321 22.34 - 33.51: 111 33.51 - 44.68: 45 44.68 - 55.85: 22 Dihedral angle restraints: 6579 sinusoidal: 2724 harmonic: 3855 Sorted by residual: dihedral pdb=" N LEU B 727 " pdb=" CA LEU B 727 " pdb=" CB LEU B 727 " pdb=" CG LEU B 727 " ideal model delta sinusoidal sigma weight residual -60.00 -107.22 47.22 3 1.50e+01 4.44e-03 8.46e+00 dihedral pdb=" N LEU C 727 " pdb=" CA LEU C 727 " pdb=" CB LEU C 727 " pdb=" CG LEU C 727 " ideal model delta sinusoidal sigma weight residual -60.00 -105.13 45.13 3 1.50e+01 4.44e-03 8.12e+00 dihedral pdb=" N LEU A 727 " pdb=" CA LEU A 727 " pdb=" CB LEU A 727 " pdb=" CG LEU A 727 " ideal model delta sinusoidal sigma weight residual -60.00 -104.89 44.89 3 1.50e+01 4.44e-03 8.07e+00 ... (remaining 6576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1098 0.025 - 0.049: 358 0.049 - 0.074: 143 0.074 - 0.099: 98 0.099 - 0.123: 52 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1746 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 714 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.31e-01 pdb=" N PRO A 715 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 714 " -0.015 5.00e-02 4.00e+02 2.21e-02 7.81e-01 pdb=" N PRO C 715 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO C 715 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 715 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 714 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.54e-01 pdb=" N PRO B 715 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO B 715 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 715 " -0.012 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2487 2.80 - 3.32: 10389 3.32 - 3.85: 16948 3.85 - 4.37: 18265 4.37 - 4.90: 32920 Nonbonded interactions: 81009 Sorted by model distance: nonbonded pdb=" OG1 THR C1100 " pdb=" O7 NAG C1302 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A1100 " pdb=" O7 NAG A1302 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B1100 " pdb=" O7 NAG B1302 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR A 837 " pdb=" OD1 ASP A 848 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR C 837 " pdb=" OD1 ASP C 848 " model vdw 2.279 3.040 ... (remaining 81004 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.340 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.090 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10578 Z= 0.135 Angle : 0.414 5.329 14433 Z= 0.210 Chirality : 0.038 0.123 1749 Planarity : 0.002 0.023 1839 Dihedral : 9.130 55.850 4044 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.72 % Allowed : 6.16 % Favored : 91.12 % 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 are not related in a simple way. whole: -0.26 (0.22), residues: 1323 helix: 2.36 (0.20), residues: 585 sheet: 1.18 (0.45), residues: 120 loop : -3.26 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 995 TYR 0.008 0.001 TYR B1067 PHE 0.006 0.001 PHE A 833 TRP 0.002 0.000 TRP A1102 HIS 0.001 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00269 (10545) covalent geometry : angle 0.41106 (14349) SS BOND : bond 0.00049 ( 15) SS BOND : angle 0.34232 ( 30) hydrogen bonds : bond 0.12606 ( 584) hydrogen bonds : angle 4.90008 ( 1716) link_NAG-ASN : bond 0.00226 ( 18) link_NAG-ASN : angle 0.91243 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8506 (mmt) cc_final: 0.7993 (mmt) REVERT: B 900 MET cc_start: 0.8627 (mmt) cc_final: 0.8190 (mmt) REVERT: C 900 MET cc_start: 0.8685 (mmt) cc_final: 0.8260 (mmt) REVERT: C 909 ILE cc_start: 0.8258 (mt) cc_final: 0.7998 (tp) outliers start: 30 outliers final: 3 residues processed: 184 average time/residue: 0.1435 time to fit residues: 34.5358 Evaluate side-chains 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 825 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN A 872 GLN A 920 GLN A 949 GLN A 992 GLN A1064 HIS A1071 GLN B 853 GLN B 872 GLN B 954 GLN B 957 GLN B 992 GLN B1064 HIS B1071 GLN C 853 GLN C 872 GLN C 992 GLN C1064 HIS C1071 GLN C1088 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.068050 restraints weight = 26826.642| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.31 r_work: 0.2534 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10578 Z= 0.165 Angle : 0.553 7.218 14433 Z= 0.288 Chirality : 0.042 0.270 1749 Planarity : 0.004 0.044 1839 Dihedral : 6.395 58.237 1782 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.17 % Allowed : 9.06 % Favored : 88.77 % 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 are not related in a simple way. whole: 0.66 (0.23), residues: 1323 helix: 3.23 (0.20), residues: 573 sheet: 1.81 (0.45), residues: 111 loop : -2.73 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1000 TYR 0.025 0.002 TYR C1067 PHE 0.018 0.002 PHE C1089 TRP 0.004 0.001 TRP A1102 HIS 0.005 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00370 (10545) covalent geometry : angle 0.54595 (14349) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.54341 ( 30) hydrogen bonds : bond 0.05171 ( 584) hydrogen bonds : angle 4.24354 ( 1716) link_NAG-ASN : bond 0.00735 ( 18) link_NAG-ASN : angle 1.53350 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7304 (p0) cc_final: 0.7046 (p0) REVERT: A 869 MET cc_start: 0.6758 (mmp) cc_final: 0.6310 (mmm) REVERT: A 900 MET cc_start: 0.8501 (mmt) cc_final: 0.7779 (mmt) REVERT: A 921 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8367 (mtmt) REVERT: B 709 ASN cc_start: 0.7144 (p0) cc_final: 0.6927 (p0) REVERT: B 900 MET cc_start: 0.8558 (mmt) cc_final: 0.7949 (mmt) REVERT: B 1125 ASN cc_start: 0.8078 (t0) cc_final: 0.7863 (t0) REVERT: C 709 ASN cc_start: 0.6823 (p0) cc_final: 0.6622 (p0) REVERT: C 900 MET cc_start: 0.8679 (mmt) cc_final: 0.8141 (mmt) REVERT: C 1083 HIS cc_start: 0.7937 (t70) cc_final: 0.7711 (t70) outliers start: 24 outliers final: 8 residues processed: 152 average time/residue: 0.1214 time to fit residues: 25.2764 Evaluate side-chains 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN A1135 ASN B 913 GLN B1135 ASN C 954 GLN C1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.098887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.062708 restraints weight = 27441.437| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 3.26 r_work: 0.2408 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10578 Z= 0.243 Angle : 0.614 7.313 14433 Z= 0.324 Chirality : 0.043 0.174 1749 Planarity : 0.004 0.043 1839 Dihedral : 5.954 58.287 1782 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.08 % Allowed : 11.23 % Favored : 85.69 % 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 are not related in a simple way. whole: 0.66 (0.23), residues: 1323 helix: 3.26 (0.20), residues: 570 sheet: 1.31 (0.41), residues: 123 loop : -2.72 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 995 TYR 0.029 0.002 TYR C1067 PHE 0.013 0.002 PHE B1089 TRP 0.005 0.001 TRP B1102 HIS 0.010 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00562 (10545) covalent geometry : angle 0.60300 (14349) SS BOND : bond 0.00388 ( 15) SS BOND : angle 0.77230 ( 30) hydrogen bonds : bond 0.05906 ( 584) hydrogen bonds : angle 4.47692 ( 1716) link_NAG-ASN : bond 0.00319 ( 18) link_NAG-ASN : angle 1.91436 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7530 (p0) cc_final: 0.7304 (p0) REVERT: A 869 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6325 (mmm) REVERT: B 900 MET cc_start: 0.8484 (mmt) cc_final: 0.8004 (mmt) REVERT: B 979 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: B 1125 ASN cc_start: 0.8196 (t0) cc_final: 0.7973 (t0) REVERT: C 861 LEU cc_start: 0.9227 (mt) cc_final: 0.8944 (mt) REVERT: C 900 MET cc_start: 0.8658 (mmt) cc_final: 0.8195 (mmt) outliers start: 34 outliers final: 16 residues processed: 145 average time/residue: 0.1072 time to fit residues: 21.7183 Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 GLN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.064431 restraints weight = 27575.471| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.29 r_work: 0.2454 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10578 Z= 0.155 Angle : 0.532 7.863 14433 Z= 0.281 Chirality : 0.041 0.182 1749 Planarity : 0.004 0.029 1839 Dihedral : 5.216 58.349 1780 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.26 % Allowed : 13.13 % Favored : 84.60 % 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 are not related in a simple way. whole: 0.97 (0.24), residues: 1323 helix: 3.53 (0.20), residues: 573 sheet: 1.44 (0.42), residues: 123 loop : -2.57 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 905 TYR 0.021 0.001 TYR C1067 PHE 0.011 0.001 PHE B1089 TRP 0.004 0.001 TRP C1102 HIS 0.012 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00346 (10545) covalent geometry : angle 0.52512 (14349) SS BOND : bond 0.00252 ( 15) SS BOND : angle 0.69434 ( 30) hydrogen bonds : bond 0.05205 ( 584) hydrogen bonds : angle 4.19690 ( 1716) link_NAG-ASN : bond 0.00631 ( 18) link_NAG-ASN : angle 1.46822 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6229 (mmm) REVERT: B 709 ASN cc_start: 0.7153 (p0) cc_final: 0.6937 (p0) REVERT: B 900 MET cc_start: 0.8435 (mmt) cc_final: 0.7984 (mmt) REVERT: B 979 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: B 1125 ASN cc_start: 0.8187 (t0) cc_final: 0.7931 (t0) REVERT: C 709 ASN cc_start: 0.6884 (p0) cc_final: 0.6678 (p0) REVERT: C 873 TYR cc_start: 0.6979 (m-10) cc_final: 0.6771 (m-10) REVERT: C 900 MET cc_start: 0.8643 (mmt) cc_final: 0.8151 (mmt) outliers start: 25 outliers final: 11 residues processed: 136 average time/residue: 0.1184 time to fit residues: 22.4566 Evaluate side-chains 117 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.061830 restraints weight = 27269.365| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 3.71 r_work: 0.2396 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10578 Z= 0.178 Angle : 0.570 7.844 14433 Z= 0.298 Chirality : 0.041 0.179 1749 Planarity : 0.004 0.035 1839 Dihedral : 5.096 56.457 1776 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.08 % Allowed : 13.04 % Favored : 83.88 % 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 are not related in a simple way. whole: 0.96 (0.24), residues: 1323 helix: 3.49 (0.20), residues: 576 sheet: 1.41 (0.42), residues: 123 loop : -2.56 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.023 0.002 TYR A1067 PHE 0.009 0.001 PHE B 970 TRP 0.005 0.001 TRP B1102 HIS 0.016 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00404 (10545) covalent geometry : angle 0.56134 (14349) SS BOND : bond 0.00274 ( 15) SS BOND : angle 0.93077 ( 30) hydrogen bonds : bond 0.05402 ( 584) hydrogen bonds : angle 4.27528 ( 1716) link_NAG-ASN : bond 0.00496 ( 18) link_NAG-ASN : angle 1.62329 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6234 (mmp) REVERT: A 900 MET cc_start: 0.8515 (mmt) cc_final: 0.7834 (mmt) REVERT: B 709 ASN cc_start: 0.7149 (p0) cc_final: 0.6922 (p0) REVERT: B 740 MET cc_start: 0.8825 (tpp) cc_final: 0.8245 (mpp) REVERT: B 900 MET cc_start: 0.8443 (mmt) cc_final: 0.8013 (mmt) REVERT: B 979 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8513 (m-30) REVERT: B 1125 ASN cc_start: 0.8206 (t0) cc_final: 0.7951 (t0) REVERT: C 709 ASN cc_start: 0.6994 (p0) cc_final: 0.6766 (p0) REVERT: C 873 TYR cc_start: 0.7050 (m-10) cc_final: 0.6797 (m-10) REVERT: C 900 MET cc_start: 0.8638 (mmt) cc_final: 0.8154 (mmt) REVERT: C 1086 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7536 (pttm) REVERT: C 1123 SER cc_start: 0.8012 (t) cc_final: 0.7769 (t) outliers start: 34 outliers final: 16 residues processed: 140 average time/residue: 0.1227 time to fit residues: 23.5561 Evaluate side-chains 129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 125 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 GLN C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.096373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.061378 restraints weight = 27942.832| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 3.18 r_work: 0.2428 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10578 Z= 0.164 Angle : 0.566 8.699 14433 Z= 0.297 Chirality : 0.041 0.171 1749 Planarity : 0.004 0.038 1839 Dihedral : 4.992 56.380 1776 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.45 % Allowed : 14.13 % Favored : 83.42 % 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 are not related in a simple way. whole: 1.07 (0.24), residues: 1323 helix: 3.57 (0.20), residues: 576 sheet: 1.88 (0.45), residues: 111 loop : -2.51 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1000 TYR 0.020 0.002 TYR A1067 PHE 0.013 0.001 PHE A 906 TRP 0.004 0.001 TRP C1102 HIS 0.014 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00370 (10545) covalent geometry : angle 0.55448 (14349) SS BOND : bond 0.00266 ( 15) SS BOND : angle 0.70593 ( 30) hydrogen bonds : bond 0.05261 ( 584) hydrogen bonds : angle 4.18897 ( 1716) link_NAG-ASN : bond 0.00494 ( 18) link_NAG-ASN : angle 1.89211 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6139 (mmp) REVERT: A 900 MET cc_start: 0.8474 (mmt) cc_final: 0.7750 (mmt) REVERT: A 1083 HIS cc_start: 0.7774 (t70) cc_final: 0.7494 (t70) REVERT: B 709 ASN cc_start: 0.7139 (p0) cc_final: 0.6915 (p0) REVERT: B 740 MET cc_start: 0.8784 (tpp) cc_final: 0.8148 (mpp) REVERT: B 826 VAL cc_start: 0.8500 (t) cc_final: 0.8210 (p) REVERT: B 900 MET cc_start: 0.8397 (mmt) cc_final: 0.7955 (mmt) REVERT: B 979 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: B 1125 ASN cc_start: 0.8220 (t0) cc_final: 0.7960 (t0) REVERT: C 709 ASN cc_start: 0.7044 (p0) cc_final: 0.6816 (p0) REVERT: C 900 MET cc_start: 0.8543 (mmt) cc_final: 0.8036 (mmt) REVERT: C 1123 SER cc_start: 0.8017 (t) cc_final: 0.7759 (t) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 0.1143 time to fit residues: 21.8229 Evaluate side-chains 127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 92 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.062015 restraints weight = 27648.813| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 3.14 r_work: 0.2432 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10578 Z= 0.161 Angle : 0.578 8.644 14433 Z= 0.303 Chirality : 0.041 0.165 1749 Planarity : 0.004 0.033 1839 Dihedral : 4.929 56.776 1776 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.72 % Allowed : 14.49 % Favored : 82.79 % 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 are not related in a simple way. whole: 1.14 (0.24), residues: 1323 helix: 3.59 (0.20), residues: 576 sheet: 1.89 (0.45), residues: 111 loop : -2.42 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.020 0.002 TYR B1067 PHE 0.010 0.001 PHE A 906 TRP 0.004 0.001 TRP C1102 HIS 0.012 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00365 (10545) covalent geometry : angle 0.56881 (14349) SS BOND : bond 0.00233 ( 15) SS BOND : angle 0.72687 ( 30) hydrogen bonds : bond 0.05235 ( 584) hydrogen bonds : angle 4.18788 ( 1716) link_NAG-ASN : bond 0.00351 ( 18) link_NAG-ASN : angle 1.73643 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6128 (mmp) REVERT: A 900 MET cc_start: 0.8489 (mmt) cc_final: 0.7796 (mmt) REVERT: B 709 ASN cc_start: 0.7141 (p0) cc_final: 0.6933 (p0) REVERT: B 740 MET cc_start: 0.8792 (tpp) cc_final: 0.8249 (mpp) REVERT: B 826 VAL cc_start: 0.8717 (t) cc_final: 0.8500 (p) REVERT: B 900 MET cc_start: 0.8429 (mmt) cc_final: 0.7995 (mmt) REVERT: B 979 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8463 (m-30) REVERT: B 1125 ASN cc_start: 0.8122 (t0) cc_final: 0.7910 (t0) REVERT: C 709 ASN cc_start: 0.6954 (p0) cc_final: 0.6736 (p0) REVERT: C 900 MET cc_start: 0.8513 (mmt) cc_final: 0.7998 (mmt) REVERT: C 921 LYS cc_start: 0.8650 (mttp) cc_final: 0.8330 (mmmm) REVERT: C 1123 SER cc_start: 0.8054 (t) cc_final: 0.7811 (t) outliers start: 30 outliers final: 18 residues processed: 136 average time/residue: 0.1151 time to fit residues: 21.8233 Evaluate side-chains 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 0.5980 chunk 112 optimal weight: 0.1980 chunk 128 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.096521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.061882 restraints weight = 27787.226| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 3.16 r_work: 0.2434 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10578 Z= 0.157 Angle : 0.582 9.926 14433 Z= 0.302 Chirality : 0.041 0.161 1749 Planarity : 0.004 0.033 1839 Dihedral : 4.903 56.348 1776 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.36 % Allowed : 14.95 % Favored : 82.70 % 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 are not related in a simple way. whole: 1.15 (0.23), residues: 1323 helix: 3.59 (0.20), residues: 576 sheet: 1.86 (0.45), residues: 111 loop : -2.39 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1000 TYR 0.020 0.002 TYR A1067 PHE 0.009 0.001 PHE A 906 TRP 0.004 0.001 TRP C1102 HIS 0.012 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00356 (10545) covalent geometry : angle 0.57241 (14349) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.72283 ( 30) hydrogen bonds : bond 0.05205 ( 584) hydrogen bonds : angle 4.17827 ( 1716) link_NAG-ASN : bond 0.00326 ( 18) link_NAG-ASN : angle 1.78170 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6541 (mmp) cc_final: 0.6210 (mmp) REVERT: A 900 MET cc_start: 0.8528 (mmt) cc_final: 0.7852 (mmt) REVERT: A 1083 HIS cc_start: 0.7536 (t70) cc_final: 0.7248 (t70) REVERT: B 740 MET cc_start: 0.8775 (tpp) cc_final: 0.8261 (mpp) REVERT: B 826 VAL cc_start: 0.8805 (t) cc_final: 0.8573 (p) REVERT: B 900 MET cc_start: 0.8444 (mmt) cc_final: 0.8023 (mmt) REVERT: B 979 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: B 1125 ASN cc_start: 0.8046 (t0) cc_final: 0.7845 (t0) REVERT: C 900 MET cc_start: 0.8493 (mmt) cc_final: 0.7963 (mmt) REVERT: C 921 LYS cc_start: 0.8623 (mttp) cc_final: 0.8405 (mmmm) REVERT: C 1123 SER cc_start: 0.8106 (t) cc_final: 0.7855 (t) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.1056 time to fit residues: 19.9405 Evaluate side-chains 129 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 7 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.061629 restraints weight = 27341.922| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 3.35 r_work: 0.2409 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10578 Z= 0.189 Angle : 0.642 10.536 14433 Z= 0.330 Chirality : 0.042 0.144 1749 Planarity : 0.004 0.039 1839 Dihedral : 5.075 56.740 1776 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.54 % Allowed : 14.95 % Favored : 82.52 % 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 are not related in a simple way. whole: 0.98 (0.23), residues: 1323 helix: 3.21 (0.20), residues: 594 sheet: 1.74 (0.44), residues: 111 loop : -2.39 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 905 TYR 0.022 0.002 TYR A1067 PHE 0.010 0.001 PHE A 906 TRP 0.004 0.001 TRP B1102 HIS 0.012 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00432 (10545) covalent geometry : angle 0.62229 (14349) SS BOND : bond 0.00265 ( 15) SS BOND : angle 0.76781 ( 30) hydrogen bonds : bond 0.05480 ( 584) hydrogen bonds : angle 4.31611 ( 1716) link_NAG-ASN : bond 0.00548 ( 18) link_NAG-ASN : angle 2.64171 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6250 (mmp) REVERT: A 900 MET cc_start: 0.8547 (mmt) cc_final: 0.7892 (mmt) REVERT: A 1083 HIS cc_start: 0.7621 (t70) cc_final: 0.7380 (t70) REVERT: B 740 MET cc_start: 0.8791 (tpp) cc_final: 0.8284 (mpp) REVERT: B 900 MET cc_start: 0.8473 (mmt) cc_final: 0.8047 (mmt) REVERT: B 979 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: C 900 MET cc_start: 0.8500 (mmt) cc_final: 0.7977 (mmt) REVERT: C 1123 SER cc_start: 0.8106 (t) cc_final: 0.7854 (t) outliers start: 28 outliers final: 20 residues processed: 132 average time/residue: 0.0817 time to fit residues: 15.1929 Evaluate side-chains 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 919 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.063247 restraints weight = 27036.757| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.35 r_work: 0.2463 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10578 Z= 0.143 Angle : 0.615 10.921 14433 Z= 0.318 Chirality : 0.041 0.207 1749 Planarity : 0.003 0.032 1839 Dihedral : 4.818 55.726 1776 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.72 % Allowed : 16.30 % Favored : 81.97 % 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 are not related in a simple way. whole: 1.17 (0.24), residues: 1323 helix: 3.38 (0.20), residues: 594 sheet: 1.85 (0.45), residues: 111 loop : -2.32 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.020 0.002 TYR C 873 PHE 0.008 0.001 PHE A1089 TRP 0.004 0.001 TRP B1102 HIS 0.010 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00320 (10545) covalent geometry : angle 0.60137 (14349) SS BOND : bond 0.00173 ( 15) SS BOND : angle 0.70776 ( 30) hydrogen bonds : bond 0.05008 ( 584) hydrogen bonds : angle 4.12335 ( 1716) link_NAG-ASN : bond 0.00517 ( 18) link_NAG-ASN : angle 2.20291 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.6227 (mmp) REVERT: A 900 MET cc_start: 0.8531 (mmt) cc_final: 0.7887 (mmt) REVERT: A 1083 HIS cc_start: 0.7427 (t70) cc_final: 0.7187 (t70) REVERT: B 740 MET cc_start: 0.8758 (tpp) cc_final: 0.8535 (mmm) REVERT: B 900 MET cc_start: 0.8431 (mmt) cc_final: 0.8061 (mmt) REVERT: C 900 MET cc_start: 0.8434 (mmt) cc_final: 0.7921 (mmt) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.1083 time to fit residues: 18.7212 Evaluate side-chains 118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.061314 restraints weight = 27254.438| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 3.33 r_work: 0.2406 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10578 Z= 0.202 Angle : 0.669 11.194 14433 Z= 0.349 Chirality : 0.043 0.192 1749 Planarity : 0.004 0.034 1839 Dihedral : 5.059 56.359 1776 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.54 % Allowed : 16.39 % Favored : 82.07 % 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 are not related in a simple way. whole: 1.03 (0.23), residues: 1323 helix: 3.44 (0.20), residues: 576 sheet: 1.65 (0.44), residues: 111 loop : -2.37 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1000 TYR 0.026 0.002 TYR A1067 PHE 0.010 0.001 PHE B 970 TRP 0.005 0.001 TRP B1102 HIS 0.011 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00466 (10545) covalent geometry : angle 0.65539 (14349) SS BOND : bond 0.00279 ( 15) SS BOND : angle 0.80649 ( 30) hydrogen bonds : bond 0.05556 ( 584) hydrogen bonds : angle 4.35353 ( 1716) link_NAG-ASN : bond 0.00463 ( 18) link_NAG-ASN : angle 2.29697 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2748.70 seconds wall clock time: 48 minutes 0.49 seconds (2880.49 seconds total)