Starting phenix.real_space_refine on Sun Sep 13 04:00:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.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/6zit_11229/09_2026/6zit_11229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.map" model { file = "/net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zit_11229/09_2026/6zit_11229.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= 0.001 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 6644 2.51 5 N 1684 2.21 5 O 1819 1.98 5 H 10483 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20683 Number of models: 1 Model: "" Number of chains: 15 Chain: "8" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 649 Classifications: {'peptide': 38} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "d" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 2534 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 142} Chain: "e" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 687 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 257 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 858 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 873 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 487 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "b" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3457 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "S" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1398 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "C" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1333 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 3.43, per 1000 atoms: 0.17 Number of scatterers: 20683 At special positions: 0 Unit cell: (94.32, 124.712, 246.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 O 1819 8.00 N 1684 7.00 C 6644 6.00 H 10483 1.00 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: 2.08 Conformation dependent library (CDL) restraints added in 598.9 milliseconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 4 sheets defined 74.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain '8' and resid 5 through 7 No H-bonds generated for 'chain '8' and resid 5 through 7' Processing helix chain '8' and resid 8 through 29 removed outlier: 4.227A pdb=" N PHE 8 24 " --> pdb=" O LEU 8 20 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 10 removed outlier: 4.380A pdb=" N SER a 8 " --> pdb=" O LEU a 5 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE a 10 " --> pdb=" O THR a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 26 removed outlier: 3.714A pdb=" N ILE a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 31 Processing helix chain 'a' and resid 40 through 59 removed outlier: 3.769A pdb=" N SER a 59 " --> pdb=" O LYS a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 87 removed outlier: 5.310A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 120 Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 120 through 128 removed outlier: 3.868A pdb=" N SER a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 136 No H-bonds generated for 'chain 'a' and resid 134 through 136' Processing helix chain 'a' and resid 137 through 182 removed outlier: 3.517A pdb=" N LEU a 141 " --> pdb=" O LEU a 137 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 3.857A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 225 removed outlier: 4.249A pdb=" N ALA a 189 " --> pdb=" O SER a 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 16 Processing helix chain 'd' and resid 17 through 19 No H-bonds generated for 'chain 'd' and resid 17 through 19' Processing helix chain 'd' and resid 20 through 22 No H-bonds generated for 'chain 'd' and resid 20 through 22' Processing helix chain 'd' and resid 23 through 44 removed outlier: 3.994A pdb=" N ALA d 27 " --> pdb=" O GLN d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 62 through 76 Processing helix chain 'd' and resid 85 through 88 Processing helix chain 'd' and resid 89 through 101 removed outlier: 4.199A pdb=" N GLU d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 Processing helix chain 'd' and resid 126 through 130 Processing helix chain 'd' and resid 131 through 139 Processing helix chain 'd' and resid 140 through 143 removed outlier: 3.560A pdb=" N LYS d 143 " --> pdb=" O PRO d 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 140 through 143' Processing helix chain 'e' and resid 7 through 42 removed outlier: 3.515A pdb=" N LYS e 11 " --> pdb=" O SER e 7 " (cutoff:3.500A) Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 10 through 14 removed outlier: 3.664A pdb=" N GLU f 13 " --> pdb=" O LYS f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 26 removed outlier: 3.576A pdb=" N LEU f 24 " --> pdb=" O PRO f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 49 Processing helix chain 'f' and resid 56 through 80 removed outlier: 3.666A pdb=" N MET f 61 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL f 62 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS f 76 " --> pdb=" O CYS f 72 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU f 77 " --> pdb=" O ARG f 73 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS f 80 " --> pdb=" O LYS f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 36 removed outlier: 3.833A pdb=" N ARG g 25 " --> pdb=" O TYR g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 61 removed outlier: 4.498A pdb=" N THR g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 Processing helix chain 'g' and resid 68 through 94 removed outlier: 3.760A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 10 Processing helix chain 'j' and resid 13 through 19 Processing helix chain 'j' and resid 21 through 46 Processing helix chain 'k' and resid 15 through 19 Processing helix chain 'k' and resid 22 through 45 Processing helix chain 'R' and resid 20 through 39 Processing helix chain 'R' and resid 42 through 74 Processing helix chain 'K' and resid 19 through 38 Processing helix chain 'K' and resid 43 through 73 Processing helix chain 'L' and resid 45 through 74 removed outlier: 3.559A pdb=" N ILE L 71 " --> pdb=" O VAL L 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 32 through 48 Processing helix chain 'b' and resid 54 through 121 removed outlier: 3.537A pdb=" N PHE b 58 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 185 removed outlier: 3.582A pdb=" N ARG b 129 " --> pdb=" O PHE b 125 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE b 159 " --> pdb=" O LEU b 155 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL b 161 " --> pdb=" O TYR b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 209 removed outlier: 3.703A pdb=" N GLN b 209 " --> pdb=" O SER b 205 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 25 removed outlier: 3.522A pdb=" N VAL h 12 " --> pdb=" O GLN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 51 removed outlier: 3.639A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 113 Processing helix chain 'S' and resid 127 through 142 Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'C' and resid 7 through 18 Processing sheet with id=AA1, first strand: chain 'b' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'S' and resid 147 through 149 removed outlier: 6.848A pdb=" N VAL S 116 " --> pdb=" O LYS S 149 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'S' and resid 147 through 149 removed outlier: 6.848A pdb=" N VAL S 116 " --> pdb=" O LYS S 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.505A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 2160 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: 4.31 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10440 1.03 - 1.23: 76 1.23 - 1.42: 4146 1.42 - 1.62: 6126 1.62 - 1.81: 99 Bond restraints: 20887 Sorted by residual: bond pdb=" CA M3L K 43 " pdb=" HA M3L K 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" CA M3L R 43 " pdb=" HA M3L R 43 " ideal model delta sigma weight residual 0.970 1.132 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" CE M3L R 43 " pdb=" HE2 M3L R 43 " ideal model delta sigma weight residual 0.970 1.129 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" CE M3L R 43 " pdb=" HE3 M3L R 43 " ideal model delta sigma weight residual 0.970 1.129 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" CE M3L K 43 " pdb=" HE3 M3L K 43 " ideal model delta sigma weight residual 0.970 1.129 -0.159 2.00e-02 2.50e+03 6.28e+01 ... (remaining 20882 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 37614 2.29 - 4.58: 305 4.58 - 6.87: 16 6.87 - 9.16: 1 9.16 - 11.44: 1 Bond angle restraints: 37937 Sorted by residual: angle pdb=" CA PRO f 5 " pdb=" N PRO f 5 " pdb=" CD PRO f 5 " ideal model delta sigma weight residual 112.00 105.89 6.11 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C ALA b 133 " pdb=" N MET b 134 " pdb=" CA MET b 134 " ideal model delta sigma weight residual 121.14 113.91 7.23 1.75e+00 3.27e-01 1.71e+01 angle pdb=" N GLY h 26 " pdb=" CA GLY h 26 " pdb=" C GLY h 26 " ideal model delta sigma weight residual 113.27 108.08 5.19 1.33e+00 5.65e-01 1.52e+01 angle pdb=" CB MET b 134 " pdb=" CG MET b 134 " pdb=" SD MET b 134 " ideal model delta sigma weight residual 112.70 101.26 11.44 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA TYR h 35 " pdb=" CB TYR h 35 " pdb=" CG TYR h 35 " ideal model delta sigma weight residual 113.90 120.17 -6.27 1.80e+00 3.09e-01 1.21e+01 ... (remaining 37932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8612 17.91 - 35.83: 821 35.83 - 53.74: 257 53.74 - 71.66: 52 71.66 - 89.57: 15 Dihedral angle restraints: 9757 sinusoidal: 5317 harmonic: 4440 Sorted by residual: dihedral pdb=" CA PHE K 73 " pdb=" C PHE K 73 " pdb=" N ALA K 74 " pdb=" CA ALA K 74 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA SER a 91 " pdb=" C SER a 91 " pdb=" N PHE a 92 " pdb=" CA PHE a 92 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY h 26 " pdb=" C GLY h 26 " pdb=" N GLY h 27 " pdb=" CA GLY h 27 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 9754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1430 0.064 - 0.129: 191 0.129 - 0.193: 7 0.193 - 0.257: 0 0.257 - 0.322: 1 Chirality restraints: 1629 Sorted by residual: chirality pdb=" CG LEU K 65 " pdb=" CB LEU K 65 " pdb=" CD1 LEU K 65 " pdb=" CD2 LEU K 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE a 106 " pdb=" CA ILE a 106 " pdb=" CG1 ILE a 106 " pdb=" CG2 ILE a 106 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA MET K 60 " pdb=" N MET K 60 " pdb=" C MET K 60 " pdb=" CB MET K 60 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1626 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 152 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO a 153 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO a 153 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 153 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 63 " 0.030 2.00e-02 2.50e+03 1.52e-02 6.91e+00 pdb=" CG PHE L 63 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE L 63 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE L 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE L 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 63 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 63 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE L 63 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE L 63 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE L 63 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE L 63 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE L 63 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG a 159 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG a 159 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG a 159 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU a 160 " -0.013 2.00e-02 2.50e+03 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1000 2.15 - 2.76: 41375 2.76 - 3.37: 60711 3.37 - 3.99: 70799 3.99 - 4.60: 111072 Nonbonded interactions: 284957 Sorted by model distance: nonbonded pdb=" OE2 GLU S 168 " pdb=" H THR C 28 " model vdw 1.535 2.450 nonbonded pdb=" OE1 GLU h 34 " pdb=" H GLU h 34 " model vdw 1.542 2.450 nonbonded pdb=" OE1 GLU d 46 " pdb=" H GLU d 46 " model vdw 1.550 2.450 nonbonded pdb="HH21 ARG S 165 " pdb=" O GLY S 167 " model vdw 1.565 2.450 nonbonded pdb=" O LEU a 149 " pdb="HE21 GLN a 152 " model vdw 1.578 2.450 ... (remaining 284952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 20 through 75)) selection = (chain 'R' and (resid 19 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 o \ r name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or n \ ame HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or nam \ e HM33)) or resid 44 through 75)) } 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: 10.660 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: 0.150 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 10404 Z= 0.257 Angle : 0.741 11.445 14063 Z= 0.426 Chirality : 0.042 0.322 1629 Planarity : 0.006 0.066 1740 Dihedral : 15.190 89.574 3838 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.92 (0.22), residues: 1264 helix: -0.68 (0.16), residues: 883 sheet: -2.13 (0.76), residues: 38 loop : -2.45 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 122 TYR 0.024 0.002 TYR h 18 PHE 0.043 0.002 PHE L 63 TRP 0.035 0.002 TRP a 109 HIS 0.008 0.002 HIS S 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 (10404) covalent geometry : angle 0.74090 / 0.43 (14063) hydrogen bonds : bond 0.14222 / 9.12 ( 737) hydrogen bonds : angle 7.38581 / 5.14 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.586 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 111 ILE cc_start: 0.8632 (mt) cc_final: 0.8412 (mm) REVERT: e 29 TYR cc_start: 0.8418 (t80) cc_final: 0.8185 (t80) REVERT: g 29 PHE cc_start: 0.7162 (m-10) cc_final: 0.6898 (m-80) REVERT: K 70 LEU cc_start: 0.8821 (mp) cc_final: 0.8607 (mm) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1813 time to fit residues: 57.6961 Evaluate side-chains 182 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 101 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 ASN ** b 114 GLN ** 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 = 0.4000 r_free = 0.4000 target = 0.086153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.078381 restraints weight = 174757.316| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.43 r_work: 0.3733 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10404 Z= 0.197 Angle : 0.669 6.075 14063 Z= 0.364 Chirality : 0.040 0.149 1629 Planarity : 0.006 0.062 1740 Dihedral : 5.634 50.546 1392 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.01 % Allowed : 9.47 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.05 (0.23), residues: 1264 helix: -0.06 (0.16), residues: 891 sheet: -2.62 (0.75), residues: 36 loop : -1.97 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 14 TYR 0.026 0.002 TYR h 35 PHE 0.026 0.002 PHE L 63 TRP 0.014 0.002 TRP d 33 HIS 0.003 0.001 HIS f 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (10404) covalent geometry : angle 0.66880 / 0.36 (14063) hydrogen bonds : bond 0.06013 / 3.87 ( 737) hydrogen bonds : angle 5.82114 / 4.11 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.631 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 TYR cc_start: 0.8604 (t80) cc_final: 0.8355 (t80) REVERT: g 29 PHE cc_start: 0.7164 (m-10) cc_final: 0.6916 (m-80) outliers start: 11 outliers final: 9 residues processed: 202 average time/residue: 0.1944 time to fit residues: 58.6118 Evaluate side-chains 193 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain f residue 85 LYS Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain S residue 144 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.086449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.078783 restraints weight = 174702.055| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.43 r_work: 0.3745 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10404 Z= 0.179 Angle : 0.629 6.826 14063 Z= 0.341 Chirality : 0.039 0.146 1629 Planarity : 0.005 0.061 1740 Dihedral : 5.424 48.924 1392 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.29 % Allowed : 12.22 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.23), residues: 1264 helix: 0.35 (0.17), residues: 893 sheet: -2.67 (0.75), residues: 36 loop : -1.82 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 14 TYR 0.020 0.002 TYR h 35 PHE 0.029 0.002 PHE L 63 TRP 0.016 0.001 TRP a 109 HIS 0.003 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (10404) covalent geometry : angle 0.62937 / 0.34 (14063) hydrogen bonds : bond 0.05595 / 3.62 ( 737) hydrogen bonds : angle 5.53318 / 3.92 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.611 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 TYR cc_start: 0.8541 (t80) cc_final: 0.8299 (t80) REVERT: g 29 PHE cc_start: 0.7160 (m-10) cc_final: 0.6881 (m-80) outliers start: 14 outliers final: 10 residues processed: 207 average time/residue: 0.1906 time to fit residues: 59.3911 Evaluate side-chains 199 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 25 GLN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** 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 = 0.4007 r_free = 0.4007 target = 0.086757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.079068 restraints weight = 174405.873| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.45 r_work: 0.3749 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10404 Z= 0.173 Angle : 0.621 9.143 14063 Z= 0.333 Chirality : 0.039 0.180 1629 Planarity : 0.005 0.060 1740 Dihedral : 5.322 48.283 1392 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.75 % Allowed : 13.14 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1264 helix: 0.61 (0.17), residues: 893 sheet: -2.62 (0.75), residues: 36 loop : -1.68 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 14 TYR 0.017 0.002 TYR b 157 PHE 0.023 0.002 PHE L 54 TRP 0.014 0.001 TRP d 33 HIS 0.003 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (10404) covalent geometry : angle 0.62078 / 0.33 (14063) hydrogen bonds : bond 0.05370 / 3.49 ( 737) hydrogen bonds : angle 5.33690 / 3.79 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.546 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 TYR cc_start: 0.8568 (t80) cc_final: 0.8320 (t80) REVERT: j 19 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7596 (tm-30) REVERT: R 58 GLU cc_start: 0.8181 (tt0) cc_final: 0.7959 (tt0) outliers start: 19 outliers final: 14 residues processed: 206 average time/residue: 0.1855 time to fit residues: 57.7220 Evaluate side-chains 200 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.087511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.079778 restraints weight = 173725.335| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.49 r_work: 0.3763 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10404 Z= 0.141 Angle : 0.598 8.451 14063 Z= 0.315 Chirality : 0.038 0.146 1629 Planarity : 0.005 0.056 1740 Dihedral : 5.126 47.403 1392 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.84 % Allowed : 13.79 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1264 helix: 0.96 (0.17), residues: 891 sheet: -2.52 (0.76), residues: 36 loop : -1.43 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 14 TYR 0.016 0.001 TYR b 157 PHE 0.025 0.001 PHE L 54 TRP 0.011 0.001 TRP d 33 HIS 0.003 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (10404) covalent geometry : angle 0.59821 / 0.32 (14063) hydrogen bonds : bond 0.05146 / 3.36 ( 737) hydrogen bonds : angle 5.08314 / 3.62 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.581 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.7654 (ttp) cc_final: 0.7305 (ppp) REVERT: a 225 ASN cc_start: 0.7828 (p0) cc_final: 0.7530 (p0) REVERT: e 29 TYR cc_start: 0.8560 (t80) cc_final: 0.8319 (t80) REVERT: j 19 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7504 (tm-30) outliers start: 20 outliers final: 16 residues processed: 202 average time/residue: 0.1910 time to fit residues: 58.4958 Evaluate side-chains 207 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 42 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.087874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.080366 restraints weight = 175123.927| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.32 r_work: 0.3780 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10404 Z= 0.141 Angle : 0.596 10.059 14063 Z= 0.312 Chirality : 0.038 0.149 1629 Planarity : 0.005 0.052 1740 Dihedral : 4.990 47.029 1392 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.56 % Allowed : 14.98 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1264 helix: 1.13 (0.17), residues: 892 sheet: -2.49 (0.76), residues: 36 loop : -1.42 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 14 TYR 0.016 0.001 TYR b 157 PHE 0.023 0.001 PHE L 54 TRP 0.011 0.001 TRP d 33 HIS 0.003 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (10404) covalent geometry : angle 0.59640 / 0.31 (14063) hydrogen bonds : bond 0.04986 / 3.27 ( 737) hydrogen bonds : angle 4.96832 / 3.53 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.610 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.7570 (ttp) cc_final: 0.7275 (ppp) REVERT: a 225 ASN cc_start: 0.7815 (p0) cc_final: 0.7505 (p0) REVERT: e 22 MET cc_start: 0.7467 (tmm) cc_final: 0.7198 (tmm) REVERT: e 29 TYR cc_start: 0.8428 (t80) cc_final: 0.8225 (t80) REVERT: g 84 MET cc_start: 0.8420 (tpp) cc_final: 0.8176 (mmt) REVERT: j 31 MET cc_start: 0.7971 (mmm) cc_final: 0.7467 (mmm) outliers start: 17 outliers final: 16 residues processed: 201 average time/residue: 0.1893 time to fit residues: 57.5622 Evaluate side-chains 204 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.0170 chunk 63 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 145 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 = 0.4038 r_free = 0.4038 target = 0.088576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.081000 restraints weight = 175068.739| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.42 r_work: 0.3789 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10404 Z= 0.132 Angle : 0.594 9.221 14063 Z= 0.307 Chirality : 0.038 0.159 1629 Planarity : 0.005 0.049 1740 Dihedral : 4.855 46.497 1392 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.02 % Allowed : 15.35 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1264 helix: 1.28 (0.17), residues: 893 sheet: -2.39 (0.78), residues: 36 loop : -1.25 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 14 TYR 0.017 0.001 TYR j 21 PHE 0.018 0.001 PHE L 54 TRP 0.011 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10404) covalent geometry : angle 0.59425 / 0.31 (14063) hydrogen bonds : bond 0.04846 / 3.19 ( 737) hydrogen bonds : angle 4.80341 / 3.43 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.562 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 161 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8312 (m) REVERT: a 182 MET cc_start: 0.7560 (ttp) cc_final: 0.7306 (ppp) REVERT: d 106 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8520 (mp10) REVERT: e 22 MET cc_start: 0.7646 (tmm) cc_final: 0.7380 (tmm) REVERT: g 87 TYR cc_start: 0.8655 (m-80) cc_final: 0.8132 (m-80) REVERT: j 31 MET cc_start: 0.7970 (mmm) cc_final: 0.7455 (mmt) REVERT: L 60 MET cc_start: 0.7099 (mmm) cc_final: 0.6859 (mmt) outliers start: 22 outliers final: 19 residues processed: 214 average time/residue: 0.1864 time to fit residues: 60.5805 Evaluate side-chains 210 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 0.0670 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN a 168 HIS ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.088872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.081276 restraints weight = 173000.967| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.43 r_work: 0.3794 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10404 Z= 0.132 Angle : 0.594 10.440 14063 Z= 0.307 Chirality : 0.039 0.164 1629 Planarity : 0.005 0.048 1740 Dihedral : 4.775 46.291 1392 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.93 % Allowed : 16.08 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1264 helix: 1.40 (0.17), residues: 893 sheet: -2.31 (0.79), residues: 36 loop : -1.20 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 14 TYR 0.016 0.001 TYR b 157 PHE 0.019 0.001 PHE L 54 TRP 0.013 0.001 TRP a 109 HIS 0.004 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (10404) covalent geometry : angle 0.59415 / 0.31 (14063) hydrogen bonds : bond 0.04735 / 3.11 ( 737) hydrogen bonds : angle 4.74840 / 3.39 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.617 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 161 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8301 (m) REVERT: a 182 MET cc_start: 0.7475 (ttp) cc_final: 0.7261 (ppp) REVERT: d 106 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8524 (mp10) REVERT: e 22 MET cc_start: 0.7635 (tmm) cc_final: 0.7343 (tmm) REVERT: g 87 TYR cc_start: 0.8684 (m-80) cc_final: 0.8158 (m-80) REVERT: j 31 MET cc_start: 0.7940 (mmm) cc_final: 0.7340 (mmm) REVERT: L 60 MET cc_start: 0.7236 (mmm) cc_final: 0.6974 (mmt) outliers start: 21 outliers final: 20 residues processed: 206 average time/residue: 0.1890 time to fit residues: 58.7689 Evaluate side-chains 209 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 130 MET Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 69 PHE Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.088184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.080599 restraints weight = 174772.987| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.37 r_work: 0.3783 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10404 Z= 0.147 Angle : 0.595 9.130 14063 Z= 0.311 Chirality : 0.039 0.177 1629 Planarity : 0.005 0.049 1740 Dihedral : 4.763 46.456 1392 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.11 % Allowed : 16.64 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1264 helix: 1.44 (0.17), residues: 893 sheet: -2.34 (0.78), residues: 36 loop : -1.21 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 14 TYR 0.016 0.001 TYR b 157 PHE 0.017 0.001 PHE L 54 TRP 0.017 0.001 TRP a 109 HIS 0.003 0.001 HIS b 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (10404) covalent geometry : angle 0.59495 / 0.31 (14063) hydrogen bonds : bond 0.04706 / 3.10 ( 737) hydrogen bonds : angle 4.76956 / 3.41 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.585 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.7480 (ttp) cc_final: 0.7277 (ppp) REVERT: d 106 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8516 (mp10) REVERT: j 31 MET cc_start: 0.7930 (mmm) cc_final: 0.7217 (mmm) outliers start: 23 outliers final: 20 residues processed: 197 average time/residue: 0.2069 time to fit residues: 60.0255 Evaluate side-chains 204 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 130 MET Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 69 PHE Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain b residue 153 ASN Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 119 optimal weight: 0.0270 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.088862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.081141 restraints weight = 169843.588| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.55 r_work: 0.3793 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10404 Z= 0.128 Angle : 0.601 9.944 14063 Z= 0.308 Chirality : 0.039 0.183 1629 Planarity : 0.005 0.048 1740 Dihedral : 4.679 46.407 1392 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.65 % Allowed : 16.91 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.11 (0.25), residues: 1264 helix: 1.54 (0.17), residues: 891 sheet: -2.26 (0.79), residues: 36 loop : -1.03 (0.38), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 159 TYR 0.015 0.001 TYR b 157 PHE 0.017 0.001 PHE L 54 TRP 0.014 0.001 TRP a 109 HIS 0.002 0.000 HIS b 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10404) covalent geometry : angle 0.60079 / 0.31 (14063) hydrogen bonds : bond 0.04643 / 3.06 ( 737) hydrogen bonds : angle 4.67732 / 3.35 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 12 is missing expected H atoms. Skipping. Residue ILE 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue TYR 21 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue VAL 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue TYR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue ILE 37 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ILE 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.606 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 161 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8277 (m) REVERT: a 182 MET cc_start: 0.7476 (ttp) cc_final: 0.7267 (ppp) REVERT: d 106 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8505 (mp10) REVERT: g 29 PHE cc_start: 0.7213 (m-10) cc_final: 0.6929 (m-80) REVERT: j 31 MET cc_start: 0.7932 (mmm) cc_final: 0.7281 (mmm) outliers start: 18 outliers final: 16 residues processed: 199 average time/residue: 0.1896 time to fit residues: 56.4083 Evaluate side-chains 202 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain a residue 161 THR Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 130 MET Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain R residue 47 PHE Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 69 PHE Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain h residue 55 MET Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 159 MET Chi-restraints excluded: chain S residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 20 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 110 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN ** b 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.089070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.081470 restraints weight = 173914.158| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.44 r_work: 0.3799 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10404 Z= 0.130 Angle : 0.593 10.676 14063 Z= 0.306 Chirality : 0.039 0.195 1629 Planarity : 0.005 0.048 1740 Dihedral : 4.623 46.381 1392 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.56 % Allowed : 17.00 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.24), residues: 1264 helix: 1.63 (0.17), residues: 891 sheet: -2.22 (0.79), residues: 36 loop : -0.95 (0.37), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 16 TYR 0.016 0.001 TYR f 66 PHE 0.016 0.001 PHE L 54 TRP 0.016 0.001 TRP a 109 HIS 0.005 0.001 HIS a 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (10404) covalent geometry : angle 0.59307 / 0.31 (14063) hydrogen bonds : bond 0.04607 / 3.03 ( 737) hydrogen bonds : angle 4.64237 / 3.33 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4702.62 seconds wall clock time: 80 minutes 46.98 seconds (4846.98 seconds total)