Starting phenix.real_space_refine on Mon Jul 28 13:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7g_39813/07_2025/8z7g_39813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7g_39813/07_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_39813/07_2025/8z7g_39813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7g_39813/07_2025/8z7g_39813.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7g_39813/07_2025/8z7g_39813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7g_39813/07_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-5711/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: 7.94, per 1000 atoms: 0.77 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: 3.01 Conformation dependent library (CDL) restraints added in 1.3 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: 1.01 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: 2.61 Time building geometry restraints manager: 3.56 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: 73.320 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.280 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.500 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 18) link_NAG-ASN : angle 0.91243 ( 54) hydrogen bonds : bond 0.12606 ( 584) hydrogen bonds : angle 4.90008 ( 1716) SS BOND : bond 0.00049 ( 15) SS BOND : angle 0.34232 ( 30) covalent geometry : bond 0.00269 (10545) covalent geometry : angle 0.41106 (14349) *********************** 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 : 1.069 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: 0.3285 time to fit residues: 81.0614 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 : 1.207 ------------------------------------------------------------------------------- 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: 0.0770 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: 7.9990 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: 0.5756 ------------------------------------------------------------------------------- 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 957 GLN B 992 GLN B1005 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 = 0.3651 r_free = 0.3651 target = 0.105255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.068982 restraints weight = 26477.958| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.32 r_work: 0.2556 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10578 Z= 0.153 Angle : 0.538 7.273 14433 Z= 0.280 Chirality : 0.042 0.304 1749 Planarity : 0.004 0.042 1839 Dihedral : 6.396 57.913 1782 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.17 % Allowed : 8.97 % Favored : 88.86 % 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: 0.69 (0.23), residues: 1323 helix: 3.27 (0.20), residues: 573 sheet: 1.85 (0.45), residues: 111 loop : -2.74 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A1102 HIS 0.005 0.002 HIS C1083 PHE 0.018 0.001 PHE C1089 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.001 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 18) link_NAG-ASN : angle 1.54511 ( 54) hydrogen bonds : bond 0.05067 ( 584) hydrogen bonds : angle 4.19473 ( 1716) SS BOND : bond 0.00203 ( 15) SS BOND : angle 0.52429 ( 30) covalent geometry : bond 0.00344 (10545) covalent geometry : angle 0.53100 (14349) *********************** 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 158 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.137 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: 0.7317 (p0) cc_final: 0.7047 (p0) REVERT: A 869 MET cc_start: 0.6835 (mmp) cc_final: 0.6372 (mmm) REVERT: A 900 MET cc_start: 0.8491 (mmt) cc_final: 0.7778 (mmt) REVERT: A 921 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8327 (mtmt) REVERT: B 709 ASN cc_start: 0.7093 (p0) cc_final: 0.6869 (p0) REVERT: B 900 MET cc_start: 0.8551 (mmt) cc_final: 0.7935 (mmt) REVERT: B 1125 ASN cc_start: 0.8084 (t0) cc_final: 0.7872 (t0) REVERT: C 873 TYR cc_start: 0.6783 (m-10) cc_final: 0.6546 (m-10) REVERT: C 900 MET cc_start: 0.8672 (mmt) cc_final: 0.8132 (mmt) REVERT: C 1083 HIS cc_start: 0.7911 (t70) cc_final: 0.7680 (t70) outliers start: 24 outliers final: 9 residues processed: 149 average time/residue: 0.2702 time to fit residues: 55.2300 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 B residue 964 LYS 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: 1.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 B 954 GLN B1005 GLN B1135 ASN C 954 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.063623 restraints weight = 27382.331| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 3.28 r_work: 0.2435 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10578 Z= 0.213 Angle : 0.587 7.633 14433 Z= 0.309 Chirality : 0.042 0.225 1749 Planarity : 0.004 0.038 1839 Dihedral : 5.838 57.816 1782 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.08 % Allowed : 10.78 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.23), residues: 1323 helix: 3.31 (0.20), residues: 573 sheet: 1.35 (0.42), residues: 123 loop : -2.69 (0.21), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B1102 HIS 0.009 0.002 HIS C1083 PHE 0.014 0.002 PHE B1089 TYR 0.027 0.002 TYR C1067 ARG 0.005 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 18) link_NAG-ASN : angle 1.74142 ( 54) hydrogen bonds : bond 0.05663 ( 584) hydrogen bonds : angle 4.38826 ( 1716) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.69747 ( 30) covalent geometry : bond 0.00488 (10545) covalent geometry : angle 0.57856 (14349) *********************** 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 154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7472 (p0) cc_final: 0.7250 (p0) REVERT: A 869 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6343 (mmm) REVERT: B 900 MET cc_start: 0.8449 (mmt) cc_final: 0.8014 (mmt) REVERT: B 979 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8511 (m-30) REVERT: B 1125 ASN cc_start: 0.8206 (t0) cc_final: 0.7968 (t0) REVERT: C 709 ASN cc_start: 0.6837 (p0) cc_final: 0.6619 (p0) REVERT: C 861 LEU cc_start: 0.9156 (mt) cc_final: 0.8859 (mt) REVERT: C 900 MET cc_start: 0.8652 (mmt) cc_final: 0.8177 (mmt) outliers start: 34 outliers final: 19 residues processed: 145 average time/residue: 0.3003 time to fit residues: 61.6556 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 1072 GLU 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 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 57 optimal weight: 0.0770 chunk 79 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.065063 restraints weight = 27061.126| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.29 r_work: 0.2477 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2952 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= 0.146 Angle : 0.521 8.002 14433 Z= 0.275 Chirality : 0.040 0.183 1749 Planarity : 0.003 0.028 1839 Dihedral : 5.136 57.578 1781 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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 (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: 1.02 (0.24), residues: 1323 helix: 3.53 (0.20), residues: 576 sheet: 1.49 (0.42), residues: 123 loop : -2.55 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.011 0.002 HIS B1083 PHE 0.012 0.001 PHE B1089 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 18) link_NAG-ASN : angle 1.39875 ( 54) hydrogen bonds : bond 0.05082 ( 584) hydrogen bonds : angle 4.14410 ( 1716) SS BOND : bond 0.00246 ( 15) SS BOND : angle 0.68284 ( 30) covalent geometry : bond 0.00325 (10545) covalent geometry : angle 0.51411 (14349) *********************** 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 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7377 (p0) cc_final: 0.7175 (p0) REVERT: A 869 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6331 (mmm) REVERT: B 709 ASN cc_start: 0.7086 (p0) cc_final: 0.6848 (p0) REVERT: B 900 MET cc_start: 0.8423 (mmt) cc_final: 0.7987 (mmt) REVERT: B 1125 ASN cc_start: 0.8180 (t0) cc_final: 0.7938 (t0) REVERT: C 709 ASN cc_start: 0.6834 (p0) cc_final: 0.6618 (p0) REVERT: C 861 LEU cc_start: 0.9183 (mt) cc_final: 0.8924 (mt) REVERT: C 873 TYR cc_start: 0.7014 (m-10) cc_final: 0.6803 (m-10) REVERT: C 900 MET cc_start: 0.8635 (mmt) cc_final: 0.8139 (mmt) outliers start: 25 outliers final: 10 residues processed: 139 average time/residue: 0.2966 time to fit residues: 58.0464 Evaluate side-chains 115 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 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 = 0.3564 r_free = 0.3564 target = 0.099257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.062847 restraints weight = 26985.431| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 3.62 r_work: 0.2407 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3196 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= 0.182 Angle : 0.561 7.796 14433 Z= 0.295 Chirality : 0.041 0.165 1749 Planarity : 0.004 0.033 1839 Dihedral : 5.065 56.512 1776 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.45 % Allowed : 13.32 % Favored : 84.24 % 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: 0.98 (0.24), residues: 1323 helix: 3.49 (0.20), residues: 576 sheet: 1.49 (0.42), residues: 123 loop : -2.56 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.009 0.002 HIS C1083 PHE 0.009 0.001 PHE B 970 TYR 0.023 0.002 TYR A1067 ARG 0.003 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 18) link_NAG-ASN : angle 1.49569 ( 54) hydrogen bonds : bond 0.05406 ( 584) hydrogen bonds : angle 4.26984 ( 1716) SS BOND : bond 0.00258 ( 15) SS BOND : angle 0.83678 ( 30) covalent geometry : bond 0.00416 (10545) covalent geometry : angle 0.55383 (14349) *********************** 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 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.097 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: 0.6748 (OUTLIER) cc_final: 0.6247 (mmp) REVERT: A 1083 HIS cc_start: 0.7928 (t70) cc_final: 0.7678 (t70) REVERT: B 709 ASN cc_start: 0.7133 (p0) cc_final: 0.6907 (p0) REVERT: B 740 MET cc_start: 0.8806 (tpp) cc_final: 0.8221 (mpp) REVERT: B 900 MET cc_start: 0.8450 (mmt) cc_final: 0.8020 (mmt) REVERT: B 979 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: B 1125 ASN cc_start: 0.8230 (t0) cc_final: 0.7970 (t0) REVERT: C 709 ASN cc_start: 0.7008 (p0) cc_final: 0.6782 (p0) REVERT: C 861 LEU cc_start: 0.9278 (mt) cc_final: 0.8983 (mt) REVERT: C 873 TYR cc_start: 0.7014 (m-10) cc_final: 0.6781 (m-10) REVERT: C 900 MET cc_start: 0.8659 (mmt) cc_final: 0.8173 (mmt) outliers start: 27 outliers final: 14 residues processed: 135 average time/residue: 0.2445 time to fit residues: 45.6363 Evaluate side-chains 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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 1118 ASP 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: 0.3980 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 0.0030 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 913 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 = 0.3579 r_free = 0.3579 target = 0.100594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.064886 restraints weight = 27265.957| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.27 r_work: 0.2457 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10578 Z= 0.149 Angle : 0.546 8.561 14433 Z= 0.288 Chirality : 0.041 0.162 1749 Planarity : 0.003 0.035 1839 Dihedral : 4.906 56.022 1776 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.54 % Allowed : 13.59 % 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 (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: 1.12 (0.24), residues: 1323 helix: 3.63 (0.20), residues: 576 sheet: 1.49 (0.42), residues: 123 loop : -2.49 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C1102 HIS 0.013 0.002 HIS A1083 PHE 0.009 0.001 PHE B1089 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 18) link_NAG-ASN : angle 1.61334 ( 54) hydrogen bonds : bond 0.05122 ( 584) hydrogen bonds : angle 4.15029 ( 1716) SS BOND : bond 0.00301 ( 15) SS BOND : angle 0.72029 ( 30) covalent geometry : bond 0.00334 (10545) covalent geometry : angle 0.53768 (14349) *********************** 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 139 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6256 (mmp) REVERT: A 900 MET cc_start: 0.8485 (mmt) cc_final: 0.7772 (mmt) REVERT: B 709 ASN cc_start: 0.6867 (p0) cc_final: 0.6666 (p0) REVERT: B 740 MET cc_start: 0.8728 (tpp) cc_final: 0.8230 (mpp) REVERT: B 900 MET cc_start: 0.8404 (mmt) cc_final: 0.7982 (mmt) REVERT: B 979 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: C 861 LEU cc_start: 0.9300 (mt) cc_final: 0.9017 (mt) REVERT: C 900 MET cc_start: 0.8629 (mmt) cc_final: 0.8096 (mmt) REVERT: C 921 LYS cc_start: 0.8718 (mttt) cc_final: 0.8400 (mmmm) outliers start: 28 outliers final: 15 residues processed: 132 average time/residue: 0.2497 time to fit residues: 46.2058 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 : 1.132 ------------------------------------------------------------------------------- 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 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 979 ASP 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 113 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 60 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 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 = 0.3565 r_free = 0.3565 target = 0.098880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.063401 restraints weight = 27558.647| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.26 r_work: 0.2449 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3415 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= 0.153 Angle : 0.569 9.640 14433 Z= 0.296 Chirality : 0.041 0.165 1749 Planarity : 0.003 0.029 1839 Dihedral : 4.886 56.434 1776 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.26 % Allowed : 14.22 % 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: 1.14 (0.24), residues: 1323 helix: 3.63 (0.20), residues: 576 sheet: 1.87 (0.45), residues: 111 loop : -2.46 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.008 0.001 HIS C1083 PHE 0.009 0.001 PHE A 906 TYR 0.019 0.002 TYR A1067 ARG 0.003 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 18) link_NAG-ASN : angle 2.12644 ( 54) hydrogen bonds : bond 0.05141 ( 584) hydrogen bonds : angle 4.14648 ( 1716) SS BOND : bond 0.00222 ( 15) SS BOND : angle 0.69652 ( 30) covalent geometry : bond 0.00343 (10545) covalent geometry : angle 0.55463 (14349) *********************** 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 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6238 (mmp) REVERT: A 900 MET cc_start: 0.8481 (mmt) cc_final: 0.7791 (mmt) REVERT: B 709 ASN cc_start: 0.6946 (p0) cc_final: 0.6741 (p0) REVERT: B 740 MET cc_start: 0.8735 (tpp) cc_final: 0.8236 (mpp) REVERT: B 826 VAL cc_start: 0.8647 (t) cc_final: 0.8406 (p) REVERT: B 900 MET cc_start: 0.8417 (mmt) cc_final: 0.7998 (mmt) REVERT: B 979 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: C 861 LEU cc_start: 0.9261 (mt) cc_final: 0.8986 (mt) REVERT: C 900 MET cc_start: 0.8639 (mmt) cc_final: 0.8103 (mmt) REVERT: C 921 LYS cc_start: 0.8732 (mttt) cc_final: 0.8454 (mmmm) outliers start: 25 outliers final: 14 residues processed: 134 average time/residue: 0.2730 time to fit residues: 49.9116 Evaluate side-chains 126 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 1106 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.062260 restraints weight = 27338.638| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.31 r_work: 0.2421 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10578 Z= 0.189 Angle : 0.611 9.993 14433 Z= 0.318 Chirality : 0.042 0.177 1749 Planarity : 0.004 0.037 1839 Dihedral : 5.040 57.129 1776 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.99 % Allowed : 14.86 % Favored : 83.15 % 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: 1.04 (0.23), residues: 1323 helix: 3.48 (0.20), residues: 576 sheet: 1.75 (0.44), residues: 111 loop : -2.42 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.007 0.002 HIS C1083 PHE 0.012 0.001 PHE A 906 TYR 0.022 0.002 TYR A1067 ARG 0.003 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 18) link_NAG-ASN : angle 2.12128 ( 54) hydrogen bonds : bond 0.05464 ( 584) hydrogen bonds : angle 4.30553 ( 1716) SS BOND : bond 0.00282 ( 15) SS BOND : angle 0.73684 ( 30) covalent geometry : bond 0.00433 (10545) covalent geometry : angle 0.59790 (14349) *********************** 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 137 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6208 (mmp) REVERT: A 900 MET cc_start: 0.8501 (mmt) cc_final: 0.7834 (mmt) REVERT: B 740 MET cc_start: 0.8754 (tpp) cc_final: 0.8262 (mpp) REVERT: B 826 VAL cc_start: 0.8767 (t) cc_final: 0.8535 (p) REVERT: B 900 MET cc_start: 0.8426 (mmt) cc_final: 0.8007 (mmt) REVERT: B 979 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8491 (m-30) REVERT: C 861 LEU cc_start: 0.9272 (mt) cc_final: 0.9029 (mt) REVERT: C 900 MET cc_start: 0.8624 (mmt) cc_final: 0.8091 (mmt) REVERT: C 921 LYS cc_start: 0.8785 (mttt) cc_final: 0.8503 (mmmm) outliers start: 22 outliers final: 16 residues processed: 133 average time/residue: 0.2483 time to fit residues: 46.1311 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 964 LYS 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 919 ASN 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 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 47 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.063174 restraints weight = 27483.694| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 3.27 r_work: 0.2442 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10578 Z= 0.159 Angle : 0.613 10.425 14433 Z= 0.316 Chirality : 0.041 0.177 1749 Planarity : 0.003 0.031 1839 Dihedral : 4.919 56.557 1776 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.99 % Allowed : 15.49 % 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 (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 (0.23), residues: 1323 helix: 3.60 (0.20), residues: 576 sheet: 1.85 (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 A1102 HIS 0.007 0.001 HIS C1083 PHE 0.011 0.001 PHE A 906 TYR 0.019 0.002 TYR C 873 ARG 0.003 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00493 ( 18) link_NAG-ASN : angle 2.54288 ( 54) hydrogen bonds : bond 0.05192 ( 584) hydrogen bonds : angle 4.19670 ( 1716) SS BOND : bond 0.00221 ( 15) SS BOND : angle 0.70670 ( 30) covalent geometry : bond 0.00361 (10545) covalent geometry : angle 0.59381 (14349) *********************** 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 137 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.103 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: 0.6528 (mmp) cc_final: 0.6195 (mmp) REVERT: A 900 MET cc_start: 0.8507 (mmt) cc_final: 0.7838 (mmt) REVERT: B 740 MET cc_start: 0.8748 (tpp) cc_final: 0.8269 (mpp) REVERT: B 826 VAL cc_start: 0.8807 (t) cc_final: 0.8580 (p) REVERT: B 900 MET cc_start: 0.8430 (mmt) cc_final: 0.8022 (mmt) REVERT: B 979 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: C 861 LEU cc_start: 0.9260 (mt) cc_final: 0.9010 (mt) REVERT: C 900 MET cc_start: 0.8662 (mmt) cc_final: 0.8142 (mmt) REVERT: C 921 LYS cc_start: 0.8763 (mttt) cc_final: 0.8505 (mmmm) outliers start: 22 outliers final: 16 residues processed: 135 average time/residue: 0.2502 time to fit residues: 46.6796 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 : 1.109 ------------------------------------------------------------------------------- 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 949 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1050 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1083 HIS ** 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 = 0.3566 r_free = 0.3566 target = 0.098729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.063123 restraints weight = 27289.746| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 3.29 r_work: 0.2451 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3655 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= 0.147 Angle : 0.600 10.069 14433 Z= 0.309 Chirality : 0.041 0.170 1749 Planarity : 0.003 0.031 1839 Dihedral : 4.824 55.879 1776 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.63 % Allowed : 15.85 % 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 (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: 1.23 (0.24), residues: 1323 helix: 3.65 (0.20), residues: 576 sheet: 1.85 (0.45), residues: 111 loop : -2.35 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1102 HIS 0.007 0.001 HIS B1083 PHE 0.011 0.001 PHE A 906 TYR 0.026 0.002 TYR C 873 ARG 0.004 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 18) link_NAG-ASN : angle 2.20922 ( 54) hydrogen bonds : bond 0.05092 ( 584) hydrogen bonds : angle 4.17619 ( 1716) SS BOND : bond 0.00193 ( 15) SS BOND : angle 0.71461 ( 30) covalent geometry : bond 0.00331 (10545) covalent geometry : angle 0.58494 (14349) ********************** 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 127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.212 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: 0.6414 (mmp) cc_final: 0.6118 (mmp) REVERT: A 900 MET cc_start: 0.8519 (mmt) cc_final: 0.7847 (mmt) REVERT: B 740 MET cc_start: 0.8761 (tpp) cc_final: 0.8309 (mpp) REVERT: B 900 MET cc_start: 0.8465 (mmt) cc_final: 0.8072 (mmt) REVERT: B 979 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8468 (m-30) REVERT: C 900 MET cc_start: 0.8640 (mmt) cc_final: 0.8124 (mmt) REVERT: C 921 LYS cc_start: 0.8754 (mttt) cc_final: 0.8470 (mmmm) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.2485 time to fit residues: 42.8074 Evaluate side-chains 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 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 916 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1106 GLN 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 126 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.062279 restraints weight = 27055.291| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.33 r_work: 0.2428 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10578 Z= 0.176 Angle : 0.645 10.993 14433 Z= 0.333 Chirality : 0.042 0.163 1749 Planarity : 0.004 0.035 1839 Dihedral : 4.938 56.262 1776 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.63 % Allowed : 15.76 % Favored : 82.61 % 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: 1.06 (0.23), residues: 1323 helix: 3.27 (0.20), residues: 594 sheet: 1.76 (0.44), residues: 111 loop : -2.33 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.007 0.001 HIS B1083 PHE 0.012 0.001 PHE A 906 TYR 0.025 0.002 TYR C 873 ARG 0.005 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 18) link_NAG-ASN : angle 2.20436 ( 54) hydrogen bonds : bond 0.05350 ( 584) hydrogen bonds : angle 4.29515 ( 1716) SS BOND : bond 0.00240 ( 15) SS BOND : angle 0.71837 ( 30) covalent geometry : bond 0.00405 (10545) covalent geometry : angle 0.63139 (14349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5791.17 seconds wall clock time: 103 minutes 5.01 seconds (6185.01 seconds total)