Starting phenix.real_space_refine on Fri Feb 14 16:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7g_39813/02_2025/8z7g_39813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7g_39813/02_2025/8z7g_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_2025/8z7g_39813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2025/8z7g_39813.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2025/8z7g_39813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7g_39813/02_2025/8z7g_39813.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP: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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP: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: 6.84, per 1000 atoms: 0.66 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: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.69 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: 2.80 Time building geometry restraints manager: 2.65 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 4.100 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: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.290 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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 10545 Z= 0.182 Angle : 0.411 5.329 14349 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP A1102 HIS 0.001 0.000 HIS C1088 PHE 0.006 0.001 PHE A 833 TYR 0.008 0.001 TYR B1067 ARG 0.001 0.000 ARG B 995 *********************** 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 : 1.032 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: 0.2996 time to fit residues: 71.8188 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 : 1.192 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.0070 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 50.0000 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 954 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 954 GLN C 992 GLN C1064 HIS C1071 GLN C1088 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.066950 restraints weight = 26574.022| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.30 r_work: 0.2505 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10545 Z= 0.275 Angle : 0.560 7.159 14349 Z= 0.295 Chirality : 0.042 0.256 1749 Planarity : 0.004 0.046 1839 Dihedral : 6.422 58.394 1782 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.17 % Allowed : 9.15 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1323 helix: 3.18 (0.20), residues: 573 sheet: 1.71 (0.44), residues: 111 loop : -2.74 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1102 HIS 0.006 0.002 HIS B1058 PHE 0.016 0.002 PHE C1089 TYR 0.025 0.002 TYR A1067 ARG 0.006 0.001 ARG C1000 *********************** 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 156 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7267 (p0) cc_final: 0.7030 (p0) REVERT: A 869 MET cc_start: 0.6787 (mmp) cc_final: 0.6339 (mmm) REVERT: A 900 MET cc_start: 0.8509 (mmt) cc_final: 0.7799 (mmt) REVERT: A 921 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8417 (mtmt) REVERT: B 709 ASN cc_start: 0.7157 (p0) cc_final: 0.6952 (p0) REVERT: B 900 MET cc_start: 0.8549 (mmt) cc_final: 0.7986 (mmt) REVERT: B 1125 ASN cc_start: 0.8075 (t0) cc_final: 0.7861 (t0) REVERT: C 873 TYR cc_start: 0.6824 (m-10) cc_final: 0.6601 (m-10) REVERT: C 900 MET cc_start: 0.8676 (mmt) cc_final: 0.8140 (mmt) REVERT: C 1083 HIS cc_start: 0.8004 (t70) cc_final: 0.7801 (t70) outliers start: 24 outliers final: 9 residues processed: 149 average time/residue: 0.2543 time to fit residues: 52.0482 Evaluate side-chains 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 920 GLN 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 94 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 38 optimal weight: 0.0870 chunk 131 optimal weight: 0.0000 chunk 120 optimal weight: 0.9990 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN B 913 GLN B1005 GLN B1135 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.066289 restraints weight = 27281.456| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.27 r_work: 0.2513 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10545 Z= 0.197 Angle : 0.506 8.983 14349 Z= 0.267 Chirality : 0.040 0.211 1749 Planarity : 0.003 0.025 1839 Dihedral : 5.486 57.610 1782 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.54 % Allowed : 11.05 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1323 helix: 3.46 (0.20), residues: 573 sheet: 1.85 (0.44), residues: 111 loop : -2.57 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C1102 HIS 0.011 0.002 HIS B1083 PHE 0.016 0.001 PHE B1089 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.001 ARG A1000 *********************** 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 150 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7288 (p0) cc_final: 0.7025 (p0) REVERT: A 869 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6276 (mmm) REVERT: A 1125 ASN cc_start: 0.7494 (t0) cc_final: 0.7287 (t0) REVERT: B 900 MET cc_start: 0.8453 (mmt) cc_final: 0.7945 (mmt) REVERT: B 979 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8496 (m-30) REVERT: B 1125 ASN cc_start: 0.8123 (t0) cc_final: 0.7842 (t0) REVERT: C 861 LEU cc_start: 0.9062 (mt) cc_final: 0.8862 (mt) REVERT: C 873 TYR cc_start: 0.6838 (m-10) cc_final: 0.6612 (m-10) REVERT: C 900 MET cc_start: 0.8638 (mmt) cc_final: 0.8149 (mmt) outliers start: 28 outliers final: 13 residues processed: 141 average time/residue: 0.2475 time to fit residues: 48.5921 Evaluate side-chains 127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 1072 GLU 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 979 ASP 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 1130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 97 optimal weight: 0.0060 chunk 81 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 913 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.065297 restraints weight = 26888.581| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.55 r_work: 0.2495 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10545 Z= 0.187 Angle : 0.501 8.583 14349 Z= 0.264 Chirality : 0.040 0.197 1749 Planarity : 0.003 0.026 1839 Dihedral : 4.927 55.087 1781 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.63 % Allowed : 12.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1323 helix: 3.64 (0.20), residues: 576 sheet: 1.60 (0.43), residues: 123 loop : -2.48 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C1102 HIS 0.008 0.001 HIS C1083 PHE 0.012 0.001 PHE B1089 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B 905 *********************** 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 147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.270 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: 0.7390 (p0) cc_final: 0.7181 (p0) REVERT: A 869 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6319 (mmm) REVERT: A 1086 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7415 (ptpp) REVERT: A 1125 ASN cc_start: 0.7510 (t0) cc_final: 0.7279 (t0) REVERT: B 740 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8285 (mpp) REVERT: B 900 MET cc_start: 0.8444 (mmt) cc_final: 0.7957 (mmt) REVERT: B 979 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8489 (m-30) REVERT: B 1125 ASN cc_start: 0.8204 (t0) cc_final: 0.7953 (t0) REVERT: C 861 LEU cc_start: 0.9126 (mt) cc_final: 0.8881 (mt) REVERT: C 900 MET cc_start: 0.8642 (mmt) cc_final: 0.8128 (mmt) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 0.2507 time to fit residues: 47.9158 Evaluate side-chains 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 1130 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET 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 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 916 LEU 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 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 12 optimal weight: 0.0020 chunk 73 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 949 GLN C 913 GLN ** C1088 HIS ** 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 = 0.3562 r_free = 0.3562 target = 0.099070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.062459 restraints weight = 26926.991| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 3.69 r_work: 0.2404 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10545 Z= 0.324 Angle : 0.591 8.753 14349 Z= 0.313 Chirality : 0.042 0.172 1749 Planarity : 0.004 0.044 1839 Dihedral : 5.329 57.297 1781 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.99 % Allowed : 12.59 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1323 helix: 3.39 (0.20), residues: 576 sheet: 1.45 (0.41), residues: 123 loop : -2.56 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.011 0.002 HIS C1083 PHE 0.010 0.002 PHE B 970 TYR 0.024 0.002 TYR A1067 ARG 0.004 0.001 ARG B 995 *********************** 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 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.962 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: 0.6739 (OUTLIER) cc_final: 0.6264 (mmp) REVERT: A 900 MET cc_start: 0.8500 (mmt) cc_final: 0.7792 (mmt) REVERT: A 1083 HIS cc_start: 0.7831 (t70) cc_final: 0.7607 (t70) REVERT: A 1125 ASN cc_start: 0.7544 (t0) cc_final: 0.7253 (t0) REVERT: B 900 MET cc_start: 0.8446 (mmt) cc_final: 0.7970 (mmt) REVERT: B 979 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8537 (m-30) REVERT: B 1125 ASN cc_start: 0.8210 (t0) cc_final: 0.7965 (t0) REVERT: C 709 ASN cc_start: 0.6802 (p0) cc_final: 0.6600 (p0) REVERT: C 861 LEU cc_start: 0.9312 (mt) cc_final: 0.9031 (mt) REVERT: C 900 MET cc_start: 0.8647 (mmt) cc_final: 0.8160 (mmt) outliers start: 33 outliers final: 15 residues processed: 131 average time/residue: 0.2607 time to fit residues: 46.2229 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 1050 MET 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 825 LYS Chi-restraints excluded: chain C residue 916 LEU 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 125 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN C 913 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.063325 restraints weight = 26901.460| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 3.22 r_work: 0.2438 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10545 Z= 0.278 Angle : 0.565 8.970 14349 Z= 0.299 Chirality : 0.041 0.176 1749 Planarity : 0.004 0.038 1839 Dihedral : 5.167 56.593 1780 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.90 % Allowed : 13.59 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1323 helix: 3.48 (0.20), residues: 576 sheet: 1.44 (0.42), residues: 123 loop : -2.49 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.010 0.002 HIS C1083 PHE 0.010 0.001 PHE B 970 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.001 ARG C 905 *********************** 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 147 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.951 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: 0.6671 (mmp) cc_final: 0.6231 (mmp) REVERT: A 900 MET cc_start: 0.8540 (mmt) cc_final: 0.7808 (mmt) REVERT: B 709 ASN cc_start: 0.6871 (p0) cc_final: 0.6651 (p0) REVERT: B 900 MET cc_start: 0.8434 (mmt) cc_final: 0.7986 (mmt) REVERT: B 979 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: B 1125 ASN cc_start: 0.8093 (t0) cc_final: 0.7872 (t0) REVERT: C 709 ASN cc_start: 0.6740 (p0) cc_final: 0.6528 (p0) REVERT: C 825 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7896 (mtmm) REVERT: C 861 LEU cc_start: 0.9309 (mt) cc_final: 0.9010 (mt) REVERT: C 900 MET cc_start: 0.8642 (mmt) cc_final: 0.8120 (mmt) REVERT: C 921 LYS cc_start: 0.8755 (mttt) cc_final: 0.8420 (mmmm) outliers start: 32 outliers final: 16 residues processed: 138 average time/residue: 0.2424 time to fit residues: 46.5913 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 : 1.094 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1072 GLU 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 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 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 113 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 762 GLN C 762 GLN ** C1088 HIS ** 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 = 0.3545 r_free = 0.3545 target = 0.096297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.061235 restraints weight = 28033.656| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 3.14 r_work: 0.2427 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10545 Z= 0.252 Angle : 0.569 8.986 14349 Z= 0.301 Chirality : 0.041 0.169 1749 Planarity : 0.004 0.034 1839 Dihedral : 5.060 56.333 1780 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.63 % Allowed : 13.68 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1323 helix: 3.54 (0.20), residues: 576 sheet: 1.87 (0.45), residues: 111 loop : -2.41 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.010 0.002 HIS B1083 PHE 0.011 0.001 PHE A 906 TYR 0.021 0.002 TYR C1067 ARG 0.003 0.001 ARG A 765 *********************** 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 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.183 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: 0.6588 (OUTLIER) cc_final: 0.6200 (mmp) REVERT: A 900 MET cc_start: 0.8509 (mmt) cc_final: 0.7823 (mmt) REVERT: B 709 ASN cc_start: 0.6788 (p0) cc_final: 0.6552 (p0) REVERT: B 826 VAL cc_start: 0.8660 (t) cc_final: 0.8420 (p) REVERT: B 900 MET cc_start: 0.8422 (mmt) cc_final: 0.7976 (mmt) REVERT: B 979 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8468 (m-30) REVERT: C 709 ASN cc_start: 0.6692 (p0) cc_final: 0.6461 (p0) REVERT: C 825 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7932 (mtmm) REVERT: C 900 MET cc_start: 0.8656 (mmt) cc_final: 0.8131 (mmt) REVERT: C 921 LYS cc_start: 0.8746 (mttt) cc_final: 0.8453 (mmmm) outliers start: 29 outliers final: 18 residues processed: 137 average time/residue: 0.2728 time to fit residues: 51.6112 Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain A residue 1050 MET 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 979 ASP Chi-restraints excluded: chain B residue 1106 GLN 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 916 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE 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 27 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** C1088 HIS ** 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 = 0.3534 r_free = 0.3534 target = 0.097262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.061435 restraints weight = 27241.493| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 3.23 r_work: 0.2393 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10545 Z= 0.323 Angle : 0.622 8.848 14349 Z= 0.329 Chirality : 0.042 0.168 1749 Planarity : 0.004 0.046 1839 Dihedral : 5.230 56.564 1780 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.72 % Allowed : 14.40 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1323 helix: 3.09 (0.20), residues: 594 sheet: 1.51 (0.42), residues: 117 loop : -2.42 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.011 0.002 HIS C1083 PHE 0.014 0.001 PHE A 906 TYR 0.023 0.002 TYR A1067 ARG 0.004 0.001 ARG C1000 *********************** 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 149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6273 (mmp) REVERT: A 900 MET cc_start: 0.8542 (mmt) cc_final: 0.7882 (mmt) REVERT: B 709 ASN cc_start: 0.6913 (p0) cc_final: 0.6684 (p0) REVERT: B 826 VAL cc_start: 0.8800 (t) cc_final: 0.8600 (p) REVERT: B 900 MET cc_start: 0.8462 (mmt) cc_final: 0.8029 (mmt) REVERT: B 979 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: C 709 ASN cc_start: 0.6819 (p0) cc_final: 0.6587 (p0) REVERT: C 900 MET cc_start: 0.8596 (mmt) cc_final: 0.8090 (mmt) REVERT: C 921 LYS cc_start: 0.8764 (mttt) cc_final: 0.8475 (mmmm) REVERT: C 1086 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7456 (pttm) REVERT: C 1123 SER cc_start: 0.8198 (t) cc_final: 0.7958 (t) outliers start: 30 outliers final: 19 residues processed: 140 average time/residue: 0.2571 time to fit residues: 49.7741 Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 949 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1114 ILE 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 979 ASP Chi-restraints excluded: chain B residue 1106 GLN 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 916 LEU 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 47 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 129 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0670 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** C1088 HIS ** 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 = 0.3573 r_free = 0.3573 target = 0.099280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.063726 restraints weight = 27468.486| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.33 r_work: 0.2460 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10545 Z= 0.209 Angle : 0.589 10.968 14349 Z= 0.307 Chirality : 0.041 0.171 1749 Planarity : 0.003 0.030 1839 Dihedral : 4.863 55.953 1776 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.81 % Allowed : 15.22 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1323 helix: 3.36 (0.20), residues: 594 sheet: 1.85 (0.46), residues: 111 loop : -2.33 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1102 HIS 0.010 0.002 HIS C1083 PHE 0.012 0.001 PHE A 906 TYR 0.025 0.002 TYR C 873 ARG 0.003 0.000 ARG A1000 *********************** 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 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6253 (mmp) REVERT: A 900 MET cc_start: 0.8536 (mmt) cc_final: 0.7855 (mmt) REVERT: B 709 ASN cc_start: 0.6687 (p0) cc_final: 0.6469 (p0) REVERT: B 900 MET cc_start: 0.8439 (mmt) cc_final: 0.8006 (mmt) REVERT: B 979 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: C 709 ASN cc_start: 0.6685 (p0) cc_final: 0.6453 (p0) REVERT: C 900 MET cc_start: 0.8519 (mmt) cc_final: 0.8019 (mmt) REVERT: C 921 LYS cc_start: 0.8731 (mttt) cc_final: 0.8488 (mmmm) outliers start: 20 outliers final: 11 residues processed: 132 average time/residue: 0.2612 time to fit residues: 47.6493 Evaluate side-chains 118 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 705 VAL 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 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 11 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** C1088 HIS ** 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 = 0.3553 r_free = 0.3553 target = 0.098443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.062628 restraints weight = 27214.532| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 3.29 r_work: 0.2426 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10545 Z= 0.252 Angle : 0.629 10.170 14349 Z= 0.325 Chirality : 0.041 0.169 1749 Planarity : 0.004 0.032 1839 Dihedral : 4.925 55.168 1776 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.54 % Allowed : 15.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1323 helix: 3.24 (0.20), residues: 594 sheet: 1.78 (0.45), residues: 111 loop : -2.32 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1102 HIS 0.010 0.002 HIS C1083 PHE 0.011 0.001 PHE A 906 TYR 0.024 0.002 TYR C 873 ARG 0.004 0.000 ARG A 765 ********************** 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 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6260 (mmp) REVERT: A 900 MET cc_start: 0.8536 (mmt) cc_final: 0.7843 (mmt) REVERT: A 921 LYS cc_start: 0.8772 (mptt) cc_final: 0.8487 (mmmt) REVERT: B 709 ASN cc_start: 0.6742 (p0) cc_final: 0.6527 (p0) REVERT: B 900 MET cc_start: 0.8457 (mmt) cc_final: 0.8010 (mmt) REVERT: B 917 TYR cc_start: 0.8185 (t80) cc_final: 0.7900 (t80) REVERT: B 921 LYS cc_start: 0.8602 (mptt) cc_final: 0.8364 (mmmt) REVERT: B 979 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: C 709 ASN cc_start: 0.6738 (p0) cc_final: 0.6502 (p0) REVERT: C 900 MET cc_start: 0.8496 (mmt) cc_final: 0.7957 (mmt) REVERT: C 921 LYS cc_start: 0.8789 (mttt) cc_final: 0.8519 (mmmm) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.2416 time to fit residues: 42.2446 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 949 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 705 VAL 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 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 126 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** 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 = 0.3549 r_free = 0.3549 target = 0.097940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.062069 restraints weight = 26999.476| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 3.54 r_work: 0.2409 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.281 10545 Z= 0.367 Angle : 0.929 59.156 14349 Z= 0.523 Chirality : 0.048 1.008 1749 Planarity : 0.004 0.035 1839 Dihedral : 4.979 55.180 1776 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 1.63 % Allowed : 15.94 % Favored : 82.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1323 helix: 3.18 (0.20), residues: 594 sheet: 1.78 (0.45), residues: 111 loop : -2.32 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.009 0.002 HIS C1083 PHE 0.010 0.001 PHE A 906 TYR 0.024 0.002 TYR C 873 ARG 0.011 0.001 ARG B 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5257.28 seconds wall clock time: 94 minutes 10.52 seconds (5650.52 seconds total)