Starting phenix.real_space_refine on Wed Feb 4 14:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wca_65858/02_2026/9wca_65858.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wca_65858/02_2026/9wca_65858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wca_65858/02_2026/9wca_65858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wca_65858/02_2026/9wca_65858.map" model { file = "/net/cci-nas-00/data/ceres_data/9wca_65858/02_2026/9wca_65858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wca_65858/02_2026/9wca_65858.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.044 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 39 5.16 5 C 6777 2.51 5 N 1878 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10827 Number of models: 1 Model: "" Number of chains: 6 Chain: "J" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2335 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain: "j" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1274 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 11, 'TRANS': 154} Chain: "Z" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2335 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain: "z" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1274 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 11, 'TRANS': 154} Chain: "F" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2335 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 11, 'TRANS': 293} Chain: "f" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1274 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 11, 'TRANS': 154} Time building chain proxies: 2.30, per 1000 atoms: 0.21 Number of scatterers: 10827 At special positions: 0 Unit cell: (100.975, 102.049, 225.582, 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 39 16.00 O 2133 8.00 N 1878 7.00 C 6777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 418.3 milliseconds 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 31 sheets defined 13.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'J' and resid 828 through 861 removed outlier: 3.616A pdb=" N LEU J 837 " --> pdb=" O GLU J 833 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR J 838 " --> pdb=" O LYS J 834 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU J 839 " --> pdb=" O VAL J 835 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP J 840 " --> pdb=" O GLU J 836 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 861 " --> pdb=" O ASP J 857 " (cutoff:3.500A) Processing helix chain 'J' and resid 1106 through 1108 No H-bonds generated for 'chain 'J' and resid 1106 through 1108' Processing helix chain 'j' and resid 49 through 62 removed outlier: 3.528A pdb=" N SER j 62 " --> pdb=" O ASP j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 104 removed outlier: 3.624A pdb=" N ASN j 103 " --> pdb=" O GLU j 100 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY j 104 " --> pdb=" O ALA j 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 100 through 104' Processing helix chain 'j' and resid 155 through 164 Processing helix chain 'Z' and resid 829 through 861 removed outlier: 3.641A pdb=" N LEU Z 837 " --> pdb=" O GLU Z 833 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR Z 838 " --> pdb=" O LYS Z 834 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU Z 839 " --> pdb=" O VAL Z 835 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP Z 840 " --> pdb=" O GLU Z 836 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA Z 861 " --> pdb=" O ASP Z 857 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1106 through 1108 No H-bonds generated for 'chain 'Z' and resid 1106 through 1108' Processing helix chain 'z' and resid 49 through 62 removed outlier: 3.547A pdb=" N SER z 62 " --> pdb=" O ASP z 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 100 through 104 removed outlier: 3.563A pdb=" N ASN z 103 " --> pdb=" O GLU z 100 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY z 104 " --> pdb=" O ALA z 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 100 through 104' Processing helix chain 'z' and resid 155 through 164 Processing helix chain 'F' and resid 829 through 836 Processing helix chain 'F' and resid 836 through 861 removed outlier: 4.001A pdb=" N ASP F 840 " --> pdb=" O GLU F 836 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 861 " --> pdb=" O ASP F 857 " (cutoff:3.500A) Processing helix chain 'F' and resid 1106 through 1108 No H-bonds generated for 'chain 'F' and resid 1106 through 1108' Processing helix chain 'f' and resid 49 through 62 removed outlier: 3.690A pdb=" N SER f 62 " --> pdb=" O ASP f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 104 removed outlier: 3.539A pdb=" N ASN f 103 " --> pdb=" O GLU f 100 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY f 104 " --> pdb=" O ALA f 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 100 through 104' Processing helix chain 'f' and resid 155 through 164 Processing sheet with id=AA1, first strand: chain 'J' and resid 863 through 867 Processing sheet with id=AA2, first strand: chain 'J' and resid 895 through 897 removed outlier: 5.994A pdb=" N PHE J 895 " --> pdb=" O ALA F 903 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE F 905 " --> pdb=" O PHE J 895 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL J 897 " --> pdb=" O ILE F 905 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 912 through 914 Processing sheet with id=AA4, first strand: chain 'J' and resid 916 through 919 Processing sheet with id=AA5, first strand: chain 'J' and resid 962 through 963 removed outlier: 6.472A pdb=" N ILE J 962 " --> pdb=" O ASN F 967 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'J' and resid 966 through 967 Processing sheet with id=AA7, first strand: chain 'J' and resid 977 through 978 Processing sheet with id=AA8, first strand: chain 'J' and resid 983 through 984 removed outlier: 6.788A pdb=" N GLN J 983 " --> pdb=" O ILE Z 978 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'J' and resid 998 through 1003 removed outlier: 5.622A pdb=" N LEU J1118 " --> pdb=" O PRO J1033 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 1079 through 1083 removed outlier: 6.591A pdb=" N GLY J1079 " --> pdb=" O LEU J1036 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU J1036 " --> pdb=" O GLY J1079 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE J1081 " --> pdb=" O PRO J1034 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER J1083 " --> pdb=" O ILE J1032 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 1014 through 1020 removed outlier: 6.201A pdb=" N VAL J1062 " --> pdb=" O ILE J1069 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 1040 through 1043 Processing sheet with id=AB4, first strand: chain 'j' and resid 68 through 69 removed outlier: 3.868A pdb=" N THR j 68 " --> pdb=" O ILE j 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER j 185 " --> pdb=" O THR j 34 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS j 30 " --> pdb=" O LEU j 189 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU j 41 " --> pdb=" O VAL j 153 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE j 112 " --> pdb=" O PHE j 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Z' and resid 863 through 867 Processing sheet with id=AB6, first strand: chain 'Z' and resid 912 through 914 Processing sheet with id=AB7, first strand: chain 'Z' and resid 916 through 919 Processing sheet with id=AB8, first strand: chain 'Z' and resid 938 through 939 removed outlier: 3.615A pdb=" N THR Z 939 " --> pdb=" O LEU F 933 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'Z' and resid 966 through 967 Processing sheet with id=AC1, first strand: chain 'Z' and resid 983 through 984 removed outlier: 6.885A pdb=" N GLN Z 983 " --> pdb=" O ILE F 978 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'Z' and resid 998 through 1003 removed outlier: 5.634A pdb=" N LEU Z1118 " --> pdb=" O PRO Z1033 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 1079 through 1083 removed outlier: 6.584A pdb=" N GLY Z1079 " --> pdb=" O LEU Z1036 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU Z1036 " --> pdb=" O GLY Z1079 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE Z1081 " --> pdb=" O PRO Z1034 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER Z1083 " --> pdb=" O ILE Z1032 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 1014 through 1020 removed outlier: 6.182A pdb=" N VAL Z1062 " --> pdb=" O ILE Z1069 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 1040 through 1043 Processing sheet with id=AC6, first strand: chain 'z' and resid 68 through 69 removed outlier: 3.733A pdb=" N THR z 68 " --> pdb=" O ILE z 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER z 185 " --> pdb=" O THR z 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLU z 41 " --> pdb=" O VAL z 153 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL z 153 " --> pdb=" O GLU z 41 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL z 148 " --> pdb=" O MET z 114 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N MET z 114 " --> pdb=" O VAL z 148 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY z 150 " --> pdb=" O ILE z 112 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR z 111 " --> pdb=" O ASN z 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 863 through 867 Processing sheet with id=AC8, first strand: chain 'F' and resid 916 through 919 Processing sheet with id=AC9, first strand: chain 'F' and resid 998 through 1003 removed outlier: 5.628A pdb=" N LEU F1118 " --> pdb=" O PRO F1033 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 1079 through 1083 removed outlier: 6.608A pdb=" N GLY F1079 " --> pdb=" O LEU F1036 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU F1036 " --> pdb=" O GLY F1079 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE F1081 " --> pdb=" O PRO F1034 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER F1083 " --> pdb=" O ILE F1032 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 1014 through 1020 removed outlier: 6.175A pdb=" N VAL F1062 " --> pdb=" O ILE F1069 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1040 through 1043 Processing sheet with id=AD4, first strand: chain 'f' and resid 68 through 69 removed outlier: 3.811A pdb=" N THR f 68 " --> pdb=" O ILE f 183 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER f 185 " --> pdb=" O THR f 34 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS f 30 " --> pdb=" O LEU f 189 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU f 41 " --> pdb=" O VAL f 153 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE f 112 " --> pdb=" O PHE f 149 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR f 111 " --> pdb=" O ASN f 130 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 0.79 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: 3645 1.34 - 1.46: 2221 1.46 - 1.58: 5093 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 11031 Sorted by residual: bond pdb=" N ILE J1131 " pdb=" CA ILE J1131 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.31e+00 bond pdb=" CB LYS Z 871 " pdb=" CG LYS Z 871 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CG LYS J 871 " pdb=" CD LYS J 871 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 bond pdb=" CB LYS J 871 " pdb=" CG LYS J 871 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CG LYS Z 871 " pdb=" CD LYS Z 871 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 ... (remaining 11026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 14823 2.77 - 5.54: 116 5.54 - 8.31: 8 8.31 - 11.08: 1 11.08 - 13.85: 1 Bond angle restraints: 14949 Sorted by residual: angle pdb=" C SER J1130 " pdb=" N ILE J1131 " pdb=" CA ILE J1131 " ideal model delta sigma weight residual 121.97 131.21 -9.24 1.80e+00 3.09e-01 2.63e+01 angle pdb=" CG1 ILE J1131 " pdb=" CB ILE J1131 " pdb=" CG2 ILE J1131 " ideal model delta sigma weight residual 110.70 96.85 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CB LYS Z 871 " pdb=" CG LYS Z 871 " pdb=" CD LYS Z 871 " ideal model delta sigma weight residual 111.30 118.61 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CB LYS J 871 " pdb=" CG LYS J 871 " pdb=" CD LYS J 871 " ideal model delta sigma weight residual 111.30 118.60 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C SER Z1130 " pdb=" N ILE Z1131 " pdb=" CA ILE Z1131 " ideal model delta sigma weight residual 121.97 127.62 -5.65 1.80e+00 3.09e-01 9.84e+00 ... (remaining 14944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5605 17.92 - 35.83: 826 35.83 - 53.75: 186 53.75 - 71.67: 30 71.67 - 89.58: 4 Dihedral angle restraints: 6651 sinusoidal: 2616 harmonic: 4035 Sorted by residual: dihedral pdb=" CA ASN F 943 " pdb=" C ASN F 943 " pdb=" N PRO F 944 " pdb=" CA PRO F 944 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN Z 943 " pdb=" C ASN Z 943 " pdb=" N PRO Z 944 " pdb=" CA PRO Z 944 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY Z 942 " pdb=" C GLY Z 942 " pdb=" N ASN Z 943 " pdb=" CA ASN Z 943 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1384 0.058 - 0.116: 267 0.116 - 0.174: 33 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CB ILE J1131 " pdb=" CA ILE J1131 " pdb=" CG1 ILE J1131 " pdb=" CG2 ILE J1131 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ASN Z 943 " pdb=" N ASN Z 943 " pdb=" C ASN Z 943 " pdb=" CB ASN Z 943 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CB ILE F1131 " pdb=" CA ILE F1131 " pdb=" CG1 ILE F1131 " pdb=" CG2 ILE F1131 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1683 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Z 863 " -0.022 2.00e-02 2.50e+03 1.78e-02 7.96e+00 pdb=" CG TRP Z 863 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP Z 863 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP Z 863 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP Z 863 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP Z 863 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Z 863 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z 863 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z 863 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP Z 863 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 950 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO J 951 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO J 951 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO J 951 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 943 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO Z 944 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO Z 944 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO Z 944 " -0.029 5.00e-02 4.00e+02 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 152 2.64 - 3.20: 9889 3.20 - 3.77: 16031 3.77 - 4.33: 21716 4.33 - 4.90: 36393 Nonbonded interactions: 84181 Sorted by model distance: nonbonded pdb=" O ASN Z 943 " pdb=" OH TYR z 146 " model vdw 2.071 3.040 nonbonded pdb=" O ASN F 943 " pdb=" OH TYR f 146 " model vdw 2.100 3.040 nonbonded pdb=" O ASN J 943 " pdb=" OH TYR j 146 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR f 85 " pdb=" OE1 GLN f 89 " model vdw 2.221 3.040 nonbonded pdb=" OG SER J1130 " pdb=" N ILE J1131 " model vdw 2.241 3.120 ... (remaining 84176 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: 0.01 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } ncs_group { reference = chain 'f' selection = chain 'j' selection = chain 'z' } 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: 6.050 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 11031 Z= 0.147 Angle : 0.628 13.852 14949 Z= 0.335 Chirality : 0.046 0.290 1686 Planarity : 0.005 0.057 1974 Dihedral : 17.388 89.582 4047 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 0.67 % Allowed : 28.00 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.22), residues: 1401 helix: 0.63 (0.38), residues: 168 sheet: 0.26 (0.29), residues: 330 loop : -1.87 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG j 116 TYR 0.012 0.001 TYR Z1011 PHE 0.013 0.001 PHE z 128 TRP 0.046 0.002 TRP Z 863 HIS 0.003 0.001 HIS f 30 Details of bonding type rmsd covalent geometry : bond 0.00333 (11031) covalent geometry : angle 0.62790 (14949) hydrogen bonds : bond 0.12048 ( 346) hydrogen bonds : angle 6.63984 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.278 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 132 average time/residue: 0.0926 time to fit residues: 17.1825 Evaluate side-chains 123 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 909 ASN Chi-restraints excluded: chain Z residue 981 ASN Chi-restraints excluded: chain z residue 78 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 99 ASN z 139 HIS F 841 ASN F 943 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111541 restraints weight = 16947.804| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.05 r_work: 0.3258 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11031 Z= 0.156 Angle : 0.585 7.848 14949 Z= 0.312 Chirality : 0.047 0.226 1686 Planarity : 0.005 0.059 1974 Dihedral : 5.419 35.556 1487 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.28 % Favored : 91.51 % Rotamer: Outliers : 3.33 % Allowed : 26.83 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1401 helix: 0.65 (0.37), residues: 174 sheet: 0.24 (0.28), residues: 333 loop : -1.89 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 844 TYR 0.017 0.001 TYR z 146 PHE 0.015 0.001 PHE j 128 TRP 0.029 0.002 TRP Z 863 HIS 0.003 0.001 HIS F 875 Details of bonding type rmsd covalent geometry : bond 0.00368 (11031) covalent geometry : angle 0.58508 (14949) hydrogen bonds : bond 0.03542 ( 346) hydrogen bonds : angle 5.39422 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.259 Fit side-chains REVERT: J 1131 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8125 (tt) REVERT: F 909 ASN cc_start: 0.7940 (p0) cc_final: 0.7462 (p0) outliers start: 40 outliers final: 27 residues processed: 152 average time/residue: 0.0859 time to fit residues: 18.5313 Evaluate side-chains 146 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1080 VAL Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain J residue 1131 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 937 THR Chi-restraints excluded: chain Z residue 1085 ILE Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 45 ASP Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 120 LYS Chi-restraints excluded: chain z residue 188 VAL Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 0.0370 chunk 131 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 27 optimal weight: 0.0170 chunk 104 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.1674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 71 HIS f 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112450 restraints weight = 17002.017| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.31 r_work: 0.3295 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11031 Z= 0.102 Angle : 0.547 7.689 14949 Z= 0.288 Chirality : 0.045 0.223 1686 Planarity : 0.005 0.060 1974 Dihedral : 5.019 37.231 1481 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.49 % Favored : 92.29 % Rotamer: Outliers : 4.17 % Allowed : 26.67 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.22), residues: 1401 helix: 0.88 (0.37), residues: 174 sheet: 0.38 (0.28), residues: 333 loop : -1.85 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG j 116 TYR 0.014 0.001 TYR z 146 PHE 0.010 0.001 PHE f 128 TRP 0.016 0.001 TRP Z 863 HIS 0.005 0.001 HIS F 875 Details of bonding type rmsd covalent geometry : bond 0.00237 (11031) covalent geometry : angle 0.54705 (14949) hydrogen bonds : bond 0.03144 ( 346) hydrogen bonds : angle 4.96261 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.419 Fit side-chains REVERT: J 937 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8220 (m) REVERT: J 1131 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8137 (tt) REVERT: f 62 SER cc_start: 0.6917 (OUTLIER) cc_final: 0.6606 (p) outliers start: 50 outliers final: 29 residues processed: 173 average time/residue: 0.0890 time to fit residues: 22.1627 Evaluate side-chains 154 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1080 VAL Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain J residue 1131 ILE Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 120 LYS Chi-restraints excluded: chain z residue 188 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 926 ASN Z 943 ASN F 841 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110376 restraints weight = 17212.809| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.00 r_work: 0.3244 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11031 Z= 0.201 Angle : 0.611 8.088 14949 Z= 0.323 Chirality : 0.048 0.265 1686 Planarity : 0.005 0.059 1974 Dihedral : 5.407 41.435 1481 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.56 % Favored : 90.22 % Rotamer: Outliers : 5.17 % Allowed : 26.17 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.22), residues: 1401 helix: 0.83 (0.37), residues: 174 sheet: 0.25 (0.29), residues: 333 loop : -1.88 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 116 TYR 0.014 0.001 TYR z 146 PHE 0.019 0.002 PHE z 128 TRP 0.028 0.002 TRP Z 863 HIS 0.003 0.001 HIS Z 875 Details of bonding type rmsd covalent geometry : bond 0.00484 (11031) covalent geometry : angle 0.61085 (14949) hydrogen bonds : bond 0.03391 ( 346) hydrogen bonds : angle 5.04076 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 130 time to evaluate : 0.487 Fit side-chains REVERT: J 1131 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8359 (tt) REVERT: F 863 TRP cc_start: 0.8414 (m100) cc_final: 0.7589 (m100) REVERT: F 909 ASN cc_start: 0.7900 (p0) cc_final: 0.7362 (p0) outliers start: 62 outliers final: 44 residues processed: 176 average time/residue: 0.1266 time to fit residues: 30.3801 Evaluate side-chains 170 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain J residue 1131 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 69 THR Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 120 LYS Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1031 MET Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1091 GLN Z 943 ASN F 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111234 restraints weight = 16947.787| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.03 r_work: 0.3245 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11031 Z= 0.138 Angle : 0.579 8.457 14949 Z= 0.304 Chirality : 0.046 0.256 1686 Planarity : 0.005 0.060 1974 Dihedral : 5.284 38.423 1481 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.57 % Favored : 92.22 % Rotamer: Outliers : 4.25 % Allowed : 27.58 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1401 helix: 0.87 (0.37), residues: 174 sheet: 0.32 (0.29), residues: 330 loop : -1.85 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG z 116 TYR 0.013 0.001 TYR z 146 PHE 0.014 0.001 PHE f 128 TRP 0.021 0.002 TRP Z 863 HIS 0.003 0.001 HIS F 875 Details of bonding type rmsd covalent geometry : bond 0.00332 (11031) covalent geometry : angle 0.57908 (14949) hydrogen bonds : bond 0.03297 ( 346) hydrogen bonds : angle 4.90339 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 time to evaluate : 0.439 Fit side-chains REVERT: J 1108 TRP cc_start: 0.5973 (m-10) cc_final: 0.5732 (m-10) REVERT: F 863 TRP cc_start: 0.8404 (m100) cc_final: 0.7682 (m100) outliers start: 51 outliers final: 43 residues processed: 162 average time/residue: 0.1098 time to fit residues: 25.1170 Evaluate side-chains 157 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 937 THR Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 1035 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 120 LYS Chi-restraints excluded: chain z residue 124 THR Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 884 MET Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1031 MET Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 144 PHE Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 87 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 0.0020 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 0.0170 overall best weight: 0.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 943 ASN F1091 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112661 restraints weight = 17000.935| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.26 r_work: 0.3303 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11031 Z= 0.101 Angle : 0.547 7.206 14949 Z= 0.287 Chirality : 0.045 0.228 1686 Planarity : 0.005 0.061 1974 Dihedral : 4.990 37.491 1481 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 3.92 % Allowed : 28.42 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.22), residues: 1401 helix: 1.05 (0.37), residues: 174 sheet: 0.45 (0.29), residues: 333 loop : -1.80 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 116 TYR 0.011 0.001 TYR z 146 PHE 0.010 0.001 PHE J 848 TRP 0.014 0.001 TRP Z 863 HIS 0.003 0.001 HIS z 168 Details of bonding type rmsd covalent geometry : bond 0.00240 (11031) covalent geometry : angle 0.54727 (14949) hydrogen bonds : bond 0.03038 ( 346) hydrogen bonds : angle 4.65935 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.445 Fit side-chains REVERT: J 1108 TRP cc_start: 0.5827 (m-10) cc_final: 0.5564 (m-10) REVERT: j 114 MET cc_start: 0.7855 (mmm) cc_final: 0.7406 (mmt) outliers start: 47 outliers final: 39 residues processed: 168 average time/residue: 0.0935 time to fit residues: 22.3744 Evaluate side-chains 159 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 111 THR Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 943 ASN Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 120 LYS Chi-restraints excluded: chain z residue 124 THR Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 884 MET Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1031 MET Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 943 ASN f 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112067 restraints weight = 16940.923| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.05 r_work: 0.3261 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11031 Z= 0.158 Angle : 0.583 7.167 14949 Z= 0.304 Chirality : 0.046 0.226 1686 Planarity : 0.005 0.059 1974 Dihedral : 5.137 38.706 1481 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.21 % Favored : 91.58 % Rotamer: Outliers : 4.25 % Allowed : 28.25 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1401 helix: 1.02 (0.37), residues: 174 sheet: 0.43 (0.30), residues: 333 loop : -1.79 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 116 TYR 0.009 0.001 TYR j 146 PHE 0.015 0.001 PHE j 128 TRP 0.027 0.002 TRP Z 863 HIS 0.002 0.001 HIS F 875 Details of bonding type rmsd covalent geometry : bond 0.00386 (11031) covalent geometry : angle 0.58255 (14949) hydrogen bonds : bond 0.03174 ( 346) hydrogen bonds : angle 4.68363 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.438 Fit side-chains REVERT: J 1108 TRP cc_start: 0.5953 (m-10) cc_final: 0.5686 (m-10) REVERT: j 114 MET cc_start: 0.7921 (mmm) cc_final: 0.7470 (mmt) REVERT: F 863 TRP cc_start: 0.8323 (m100) cc_final: 0.7592 (m100) outliers start: 51 outliers final: 42 residues processed: 161 average time/residue: 0.1020 time to fit residues: 23.0988 Evaluate side-chains 159 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 1015 THR Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 1035 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 45 ASP Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 120 LYS Chi-restraints excluded: chain z residue 124 THR Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 884 MET Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1031 MET Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 943 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112288 restraints weight = 17052.932| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.95 r_work: 0.3256 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11031 Z= 0.159 Angle : 0.593 7.182 14949 Z= 0.309 Chirality : 0.046 0.219 1686 Planarity : 0.005 0.061 1974 Dihedral : 5.211 39.096 1481 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 4.08 % Allowed : 28.00 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.22), residues: 1401 helix: 1.02 (0.37), residues: 174 sheet: 0.39 (0.30), residues: 330 loop : -1.80 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 116 TYR 0.011 0.001 TYR z 146 PHE 0.015 0.001 PHE f 128 TRP 0.028 0.002 TRP Z 863 HIS 0.002 0.001 HIS Z 875 Details of bonding type rmsd covalent geometry : bond 0.00385 (11031) covalent geometry : angle 0.59345 (14949) hydrogen bonds : bond 0.03262 ( 346) hydrogen bonds : angle 4.74860 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.275 Fit side-chains REVERT: J 1108 TRP cc_start: 0.5973 (m-10) cc_final: 0.5663 (m-10) REVERT: j 114 MET cc_start: 0.7891 (mmm) cc_final: 0.7440 (mmt) REVERT: F 863 TRP cc_start: 0.8347 (m100) cc_final: 0.7700 (m100) outliers start: 49 outliers final: 43 residues processed: 158 average time/residue: 0.1000 time to fit residues: 21.9242 Evaluate side-chains 160 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 1015 THR Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 1035 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 124 THR Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 884 MET Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 144 PHE Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 943 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111292 restraints weight = 16964.976| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.01 r_work: 0.3233 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11031 Z= 0.157 Angle : 0.606 8.222 14949 Z= 0.316 Chirality : 0.046 0.210 1686 Planarity : 0.005 0.061 1974 Dihedral : 5.274 39.298 1481 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.49 % Favored : 91.29 % Rotamer: Outliers : 4.33 % Allowed : 28.00 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.22), residues: 1401 helix: 0.93 (0.37), residues: 174 sheet: 0.27 (0.30), residues: 330 loop : -1.80 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG j 116 TYR 0.013 0.001 TYR z 146 PHE 0.015 0.001 PHE f 128 TRP 0.030 0.002 TRP Z 863 HIS 0.002 0.001 HIS Z 875 Details of bonding type rmsd covalent geometry : bond 0.00380 (11031) covalent geometry : angle 0.60588 (14949) hydrogen bonds : bond 0.03315 ( 346) hydrogen bonds : angle 4.78747 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.343 Fit side-chains REVERT: J 1108 TRP cc_start: 0.5993 (m-10) cc_final: 0.5722 (m-10) REVERT: j 114 MET cc_start: 0.7931 (mmm) cc_final: 0.7483 (mmt) REVERT: F 863 TRP cc_start: 0.8350 (m100) cc_final: 0.7710 (m100) REVERT: F 909 ASN cc_start: 0.7969 (p0) cc_final: 0.7243 (p0) outliers start: 52 outliers final: 45 residues processed: 162 average time/residue: 0.0973 time to fit residues: 21.7926 Evaluate side-chains 159 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 1015 THR Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1069 ILE Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 112 ILE Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 1035 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain Z residue 1115 SER Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 124 THR Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 870 THR Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 112 ILE Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 943 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111006 restraints weight = 16907.534| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.35 r_work: 0.3283 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11031 Z= 0.113 Angle : 0.587 7.593 14949 Z= 0.304 Chirality : 0.045 0.185 1686 Planarity : 0.005 0.062 1974 Dihedral : 5.104 37.691 1481 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.99 % Favored : 91.79 % Rotamer: Outliers : 3.25 % Allowed : 29.00 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.22), residues: 1401 helix: 1.21 (0.38), residues: 168 sheet: 0.35 (0.30), residues: 330 loop : -1.76 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 116 TYR 0.012 0.001 TYR z 146 PHE 0.011 0.001 PHE f 128 TRP 0.019 0.001 TRP Z 863 HIS 0.003 0.001 HIS F 875 Details of bonding type rmsd covalent geometry : bond 0.00276 (11031) covalent geometry : angle 0.58665 (14949) hydrogen bonds : bond 0.03140 ( 346) hydrogen bonds : angle 4.65529 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.375 Fit side-chains REVERT: j 114 MET cc_start: 0.7869 (mmm) cc_final: 0.7408 (mmt) REVERT: f 156 MET cc_start: 0.7022 (mmt) cc_final: 0.6415 (mmt) outliers start: 39 outliers final: 36 residues processed: 155 average time/residue: 0.0865 time to fit residues: 19.3722 Evaluate side-chains 155 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 841 ASN Chi-restraints excluded: chain J residue 859 TRP Chi-restraints excluded: chain J residue 905 ILE Chi-restraints excluded: chain J residue 909 ASN Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 1018 VAL Chi-restraints excluded: chain J residue 1057 THR Chi-restraints excluded: chain J residue 1085 ILE Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 78 MET Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 133 ASP Chi-restraints excluded: chain j residue 153 VAL Chi-restraints excluded: chain j residue 170 VAL Chi-restraints excluded: chain Z residue 837 LEU Chi-restraints excluded: chain Z residue 841 ASN Chi-restraints excluded: chain Z residue 905 ILE Chi-restraints excluded: chain Z residue 917 VAL Chi-restraints excluded: chain Z residue 1057 THR Chi-restraints excluded: chain z residue 31 VAL Chi-restraints excluded: chain z residue 78 MET Chi-restraints excluded: chain z residue 79 ILE Chi-restraints excluded: chain z residue 99 ASN Chi-restraints excluded: chain z residue 124 THR Chi-restraints excluded: chain z residue 170 VAL Chi-restraints excluded: chain F residue 837 LEU Chi-restraints excluded: chain F residue 841 ASN Chi-restraints excluded: chain F residue 870 THR Chi-restraints excluded: chain F residue 917 VAL Chi-restraints excluded: chain F residue 1057 THR Chi-restraints excluded: chain F residue 1080 VAL Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 133 ASP Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 170 VAL Chi-restraints excluded: chain f residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 0.0030 chunk 8 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 0.1366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 841 ASN Z 943 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114985 restraints weight = 17003.108| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.30 r_work: 0.3317 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11031 Z= 0.102 Angle : 0.575 7.378 14949 Z= 0.297 Chirality : 0.045 0.177 1686 Planarity : 0.005 0.063 1974 Dihedral : 4.903 37.739 1481 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.21 % Favored : 91.58 % Rotamer: Outliers : 2.92 % Allowed : 29.58 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1401 helix: 1.14 (0.38), residues: 168 sheet: 0.44 (0.30), residues: 333 loop : -1.75 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 116 TYR 0.013 0.001 TYR Z1053 PHE 0.009 0.001 PHE f 128 TRP 0.022 0.001 TRP Z 863 HIS 0.005 0.001 HIS F 875 Details of bonding type rmsd covalent geometry : bond 0.00248 (11031) covalent geometry : angle 0.57472 (14949) hydrogen bonds : bond 0.02971 ( 346) hydrogen bonds : angle 4.52105 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.14 seconds wall clock time: 40 minutes 16.17 seconds (2416.17 seconds total)