Starting phenix.real_space_refine on Tue Mar 3 20:07:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fje_31619/03_2026/7fje_31619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fje_31619/03_2026/7fje_31619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2026/7fje_31619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2026/7fje_31619.map" model { file = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2026/7fje_31619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2026/7fje_31619.cif" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5322 2.51 5 N 1370 2.21 5 O 1592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8338 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 264 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "b" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "d" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "e" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "f" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 949 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1924 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 233} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2240 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 271} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8338 At special positions: 0 Unit cell: (92.4, 97.9, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1592 8.00 N 1370 7.00 C 5322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.02 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.04 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.04 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Simple disulfide: pdb=" SG CYS m 45 " - pdb=" SG CYS m 111 " distance=2.04 Simple disulfide: pdb=" SG CYS m 155 " - pdb=" SG CYS m 205 " distance=2.03 Simple disulfide: pdb=" SG CYS m 227 " - pdb=" SG CYS n 264 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 110 " distance=2.04 Simple disulfide: pdb=" SG CYS n 164 " - pdb=" SG CYS n 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 248.9 milliseconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 19 sheets defined 25.7% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'a' and resid 28 through 54 removed outlier: 4.484A pdb=" N CYS a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU a 39 " --> pdb=" O LEU a 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 51 removed outlier: 3.634A pdb=" N ILE b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU b 39 " --> pdb=" O LEU b 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 66 No H-bonds generated for 'chain 'd' and resid 64 through 66' Processing helix chain 'd' and resid 102 through 123 removed outlier: 4.136A pdb=" N PHE d 123 " --> pdb=" O ALA d 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 108 removed outlier: 3.595A pdb=" N ASP e 107 " --> pdb=" O LYS e 104 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA e 108 " --> pdb=" O PRO e 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 104 through 108' Processing helix chain 'e' and resid 127 through 154 removed outlier: 3.646A pdb=" N ALA e 131 " --> pdb=" O VAL e 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 4.034A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 104 through 108' Processing helix chain 'f' and resid 128 through 154 removed outlier: 4.525A pdb=" N GLY f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU f 144 " --> pdb=" O ILE f 140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU f 145 " --> pdb=" O THR f 141 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU f 146 " --> pdb=" O GLY f 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 138 removed outlier: 3.734A pdb=" N ILE g 115 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY g 138 " --> pdb=" O TYR g 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 106 removed outlier: 3.652A pdb=" N ASP m 105 " --> pdb=" O GLN m 102 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER m 106 " --> pdb=" O PRO m 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 102 through 106' Processing helix chain 'm' and resid 231 through 235 Processing helix chain 'm' and resid 239 through 273 removed outlier: 3.787A pdb=" N ASN m 243 " --> pdb=" O ASP m 239 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE m 254 " --> pdb=" O ILE m 250 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU m 268 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG m 269 " --> pdb=" O LEU m 265 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU m 270 " --> pdb=" O MET m 266 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP m 271 " --> pdb=" O THR m 267 " (cutoff:3.500A) Processing helix chain 'n' and resid 135 through 139 removed outlier: 3.722A pdb=" N ASN n 138 " --> pdb=" O ASP n 135 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL n 139 " --> pdb=" O LEU n 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 135 through 139' Processing helix chain 'n' and resid 150 through 157 Processing helix chain 'n' and resid 217 through 221 Processing helix chain 'n' and resid 270 through 307 Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 27 removed outlier: 5.814A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 5.419A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER d 84 " --> pdb=" O CYS d 73 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE e 66 " --> pdb=" O TRP e 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40 removed outlier: 3.785A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 40 Processing sheet with id=AA6, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.626A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE g 53 " --> pdb=" O PHE g 64 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE g 64 " --> pdb=" O ILE g 53 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.582A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.670A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR m 54 " --> pdb=" O SER m 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE m 55 " --> pdb=" O TYR m 71 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR m 71 " --> pdb=" O PHE m 55 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP m 57 " --> pdb=" O LEU m 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'm' and resid 33 through 36 removed outlier: 3.670A pdb=" N LEU m 33 " --> pdb=" O MET m 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 40 through 45 removed outlier: 3.510A pdb=" N TYR m 93 " --> pdb=" O ASP m 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 140 through 143 removed outlier: 3.859A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 140 through 143 removed outlier: 3.859A pdb=" N ALA m 140 " --> pdb=" O THR m 158 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER m 153 " --> pdb=" O SER m 198 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER m 198 " --> pdb=" O SER m 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 23 through 26 Processing sheet with id=AB6, first strand: chain 'n' and resid 29 through 32 Processing sheet with id=AB7, first strand: chain 'n' and resid 73 through 76 removed outlier: 7.105A pdb=" N ILE n 73 " --> pdb=" O VAL n 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL n 69 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR n 67 " --> pdb=" O ASP n 75 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY n 61 " --> pdb=" O ASP n 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP n 57 " --> pdb=" O GLY n 61 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP n 53 " --> pdb=" O ILE n 65 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR n 67 " --> pdb=" O MET n 51 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET n 51 " --> pdb=" O TYR n 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA n 111 " --> pdb=" O SER n 52 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL n 107 " --> pdb=" O GLN n 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.520A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER n 190 " --> pdb=" O ARG n 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 143 through 147 removed outlier: 5.520A pdb=" N TYR n 207 " --> pdb=" O GLY n 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'n' and resid 183 through 184 383 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2553 1.34 - 1.47: 2224 1.47 - 1.60: 3666 1.60 - 1.73: 0 1.73 - 1.86: 76 Bond restraints: 8519 Sorted by residual: bond pdb=" CA TYR d 79 " pdb=" C TYR d 79 " ideal model delta sigma weight residual 1.523 1.586 -0.063 1.34e-02 5.57e+03 2.20e+01 bond pdb=" C SER e 103 " pdb=" N LYS e 104 " ideal model delta sigma weight residual 1.327 1.233 0.094 2.86e-02 1.22e+03 1.09e+01 bond pdb=" CA SER m 235 " pdb=" CB SER m 235 " ideal model delta sigma weight residual 1.531 1.434 0.097 3.12e-02 1.03e+03 9.61e+00 bond pdb=" CG LEU f 114 " pdb=" CD2 LEU f 114 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB ARG n 228 " pdb=" CG ARG n 228 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 ... (remaining 8514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 11309 3.26 - 6.53: 211 6.53 - 9.79: 29 9.79 - 13.05: 6 13.05 - 16.31: 3 Bond angle restraints: 11558 Sorted by residual: angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.08 -15.74 2.08e+00 2.31e-01 5.73e+01 angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" CA TYR d 79 " pdb=" C TYR d 79 " pdb=" O TYR d 79 " ideal model delta sigma weight residual 120.51 113.15 7.36 1.43e+00 4.89e-01 2.65e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.21 -12.41 2.44e+00 1.68e-01 2.59e+01 angle pdb=" C GLU g 67 " pdb=" N ASP g 68 " pdb=" CA ASP g 68 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 11553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4828 16.48 - 32.97: 228 32.97 - 49.45: 89 49.45 - 65.93: 9 65.93 - 82.42: 8 Dihedral angle restraints: 5162 sinusoidal: 2086 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.66 52.34 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -131.28 -48.72 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1071 0.086 - 0.173: 212 0.173 - 0.259: 13 0.259 - 0.346: 2 0.346 - 0.432: 1 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CG LEU a 27 " pdb=" CB LEU a 27 " pdb=" CD1 LEU a 27 " pdb=" CD2 LEU a 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1296 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.019 2.00e-02 2.50e+03 2.10e-02 8.85e+00 pdb=" CG TYR e 111 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.021 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR d 90 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN n 194 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO n 195 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO n 195 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO n 195 " 0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2178 2.81 - 3.33: 6444 3.33 - 3.85: 12226 3.85 - 4.38: 13205 4.38 - 4.90: 24282 Nonbonded interactions: 58335 Sorted by model distance: nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.287 3.040 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.391 3.120 nonbonded pdb=" OG SER a 23 " pdb=" OE1 GLN d 94 " model vdw 2.405 3.040 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.441 3.120 nonbonded pdb=" O PHE a 24 " pdb=" OG1 THR m 238 " model vdw 2.451 3.040 ... (remaining 58330 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 'a' and resid 26 through 54) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 155)) selection = (chain 'f' and resid 33 through 155) } 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: 0.990 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.010 0.109 8532 Z= 0.415 Angle : 1.197 16.314 11584 Z= 0.642 Chirality : 0.066 0.432 1299 Planarity : 0.008 0.060 1468 Dihedral : 11.624 76.759 3149 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.97 % Allowed : 5.62 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -3.03 (0.22), residues: 1040 helix: -0.57 (0.31), residues: 231 sheet: -1.05 (0.32), residues: 234 loop : -3.21 (0.19), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 117 TYR 0.051 0.005 TYR e 111 PHE 0.036 0.004 PHE n 29 TRP 0.026 0.004 TRP m 197 HIS 0.016 0.004 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00983 ( 8519) covalent geometry : angle 1.19248 (11558) SS BOND : bond 0.00655 ( 13) SS BOND : angle 2.42578 ( 26) hydrogen bonds : bond 0.26696 ( 356) hydrogen bonds : angle 7.26966 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8289 (tppp) cc_final: 0.7567 (tmmm) REVERT: d 117 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7575 (tp) REVERT: e 85 LYS cc_start: 0.8689 (mttt) cc_final: 0.8482 (mmmm) REVERT: e 103 SER cc_start: 0.9035 (t) cc_final: 0.8765 (m) REVERT: e 121 ASN cc_start: 0.7809 (m110) cc_final: 0.7365 (m-40) REVERT: e 124 GLU cc_start: 0.8648 (tt0) cc_final: 0.8444 (tt0) REVERT: e 128 MET cc_start: 0.7390 (mmm) cc_final: 0.6975 (mmt) REVERT: f 51 GLN cc_start: 0.8306 (mt0) cc_final: 0.8041 (mp10) REVERT: f 104 LYS cc_start: 0.9093 (mttt) cc_final: 0.8807 (mmmt) REVERT: f 127 VAL cc_start: 0.8708 (m) cc_final: 0.8478 (p) REVERT: m 188 ASP cc_start: 0.7712 (t0) cc_final: 0.7380 (t70) REVERT: n 33 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8136 (tttt) REVERT: n 121 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6868 (tt0) REVERT: n 135 ASP cc_start: 0.8430 (t70) cc_final: 0.8166 (t0) outliers start: 9 outliers final: 1 residues processed: 227 average time/residue: 0.4722 time to fit residues: 114.1737 Evaluate side-chains 147 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN f 65 ASN f 74 ASN f 121 ASN g 37 GLN m 86 GLN n 25 GLN n 47 ASN n 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093081 restraints weight = 11269.917| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.86 r_work: 0.2921 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8532 Z= 0.155 Angle : 0.705 10.545 11584 Z= 0.369 Chirality : 0.045 0.228 1299 Planarity : 0.005 0.050 1468 Dihedral : 6.605 59.786 1212 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.58 % Favored : 94.23 % Rotamer: Outliers : 3.78 % Allowed : 12.74 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.49 (0.24), residues: 1040 helix: 1.96 (0.33), residues: 238 sheet: -0.06 (0.33), residues: 252 loop : -3.00 (0.20), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG m 145 TYR 0.024 0.002 TYR n 50 PHE 0.017 0.002 PHE m 157 TRP 0.015 0.002 TRP m 197 HIS 0.004 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8519) covalent geometry : angle 0.69818 (11558) SS BOND : bond 0.00365 ( 13) SS BOND : angle 2.10781 ( 26) hydrogen bonds : bond 0.06922 ( 356) hydrogen bonds : angle 4.55982 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8161 (tppp) cc_final: 0.7334 (tmmm) REVERT: d 29 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8053 (mt) REVERT: e 39 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8499 (m) REVERT: e 85 LYS cc_start: 0.8782 (mttt) cc_final: 0.8546 (mmmm) REVERT: e 103 SER cc_start: 0.8963 (t) cc_final: 0.8729 (m) REVERT: e 104 LYS cc_start: 0.8932 (mtpm) cc_final: 0.8652 (mtmp) REVERT: e 125 MET cc_start: 0.8749 (tpp) cc_final: 0.8472 (mmm) REVERT: e 128 MET cc_start: 0.7409 (mmm) cc_final: 0.7044 (mmt) REVERT: f 56 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: f 104 LYS cc_start: 0.9249 (mttt) cc_final: 0.8794 (mmmt) REVERT: g 105 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: m 53 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: m 71 TYR cc_start: 0.7004 (t80) cc_final: 0.5147 (t80) REVERT: m 188 ASP cc_start: 0.8435 (t0) cc_final: 0.8073 (t70) REVERT: m 233 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8215 (tt0) REVERT: n 33 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8110 (tttt) REVERT: n 121 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6739 (mp0) REVERT: n 123 TYR cc_start: 0.7579 (m-80) cc_final: 0.7323 (m-80) REVERT: n 135 ASP cc_start: 0.8677 (t70) cc_final: 0.8386 (t0) outliers start: 35 outliers final: 18 residues processed: 190 average time/residue: 0.4531 time to fit residues: 92.1570 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 90 SER Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 245 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 0.0000 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 61 HIS f 51 GLN f 74 ASN g 52 ASN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.094301 restraints weight = 11208.611| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.87 r_work: 0.2933 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8532 Z= 0.126 Angle : 0.618 10.374 11584 Z= 0.325 Chirality : 0.043 0.211 1299 Planarity : 0.004 0.045 1468 Dihedral : 5.828 63.392 1208 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.35 % Favored : 93.46 % Rotamer: Outliers : 4.21 % Allowed : 15.44 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.77 (0.25), residues: 1040 helix: 2.91 (0.32), residues: 240 sheet: 0.40 (0.33), residues: 260 loop : -2.80 (0.21), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.020 0.002 TYR g 34 PHE 0.014 0.001 PHE m 157 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8519) covalent geometry : angle 0.61508 (11558) SS BOND : bond 0.00358 ( 13) SS BOND : angle 1.48004 ( 26) hydrogen bonds : bond 0.05504 ( 356) hydrogen bonds : angle 4.05654 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8195 (tppp) cc_final: 0.7346 (tmmm) REVERT: d 29 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7810 (mp) REVERT: e 85 LYS cc_start: 0.8864 (mttt) cc_final: 0.8578 (mmmm) REVERT: e 103 SER cc_start: 0.8945 (t) cc_final: 0.8732 (m) REVERT: e 104 LYS cc_start: 0.8918 (mtpm) cc_final: 0.8653 (mtmp) REVERT: e 121 ASN cc_start: 0.7924 (m110) cc_final: 0.7295 (m-40) REVERT: e 128 MET cc_start: 0.7152 (mmm) cc_final: 0.6817 (mmt) REVERT: f 56 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: f 104 LYS cc_start: 0.9239 (mttt) cc_final: 0.8821 (mmmt) REVERT: f 128 MET cc_start: 0.7182 (ttt) cc_final: 0.6704 (mmt) REVERT: f 135 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7870 (mp) REVERT: f 140 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7756 (mp) REVERT: m 47 TYR cc_start: 0.8555 (p90) cc_final: 0.8219 (p90) REVERT: m 53 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: m 71 TYR cc_start: 0.6927 (t80) cc_final: 0.5434 (t80) REVERT: m 188 ASP cc_start: 0.8416 (t0) cc_final: 0.8051 (t70) REVERT: m 211 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8735 (t0) REVERT: m 233 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8149 (tt0) REVERT: n 33 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8389 (ttmm) REVERT: n 121 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6879 (mp0) REVERT: n 123 TYR cc_start: 0.7810 (m-80) cc_final: 0.7410 (m-80) REVERT: n 135 ASP cc_start: 0.8665 (t70) cc_final: 0.8392 (t0) REVERT: n 137 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8522 (mtmm) outliers start: 39 outliers final: 19 residues processed: 174 average time/residue: 0.5103 time to fit residues: 94.4070 Evaluate side-chains 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 29 HIS m 163 GLN m 168 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093993 restraints weight = 11485.829| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.91 r_work: 0.2917 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8532 Z= 0.122 Angle : 0.600 10.456 11584 Z= 0.314 Chirality : 0.042 0.195 1299 Planarity : 0.004 0.042 1468 Dihedral : 5.482 59.325 1208 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 4.43 % Allowed : 16.31 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.37 (0.26), residues: 1040 helix: 3.47 (0.31), residues: 237 sheet: 0.82 (0.33), residues: 259 loop : -2.74 (0.21), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 101 TYR 0.025 0.001 TYR m 93 PHE 0.017 0.001 PHE m 55 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS g 29 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8519) covalent geometry : angle 0.59731 (11558) SS BOND : bond 0.00319 ( 13) SS BOND : angle 1.27582 ( 26) hydrogen bonds : bond 0.05149 ( 356) hydrogen bonds : angle 3.88575 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8213 (tppp) cc_final: 0.7318 (tmmm) REVERT: d 29 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7794 (mp) REVERT: d 92 MET cc_start: 0.8581 (mmm) cc_final: 0.7957 (mmm) REVERT: e 85 LYS cc_start: 0.8882 (mttt) cc_final: 0.8554 (mmmm) REVERT: e 103 SER cc_start: 0.8931 (t) cc_final: 0.8691 (m) REVERT: e 104 LYS cc_start: 0.8883 (mtpm) cc_final: 0.8669 (mtmp) REVERT: e 121 ASN cc_start: 0.7855 (m110) cc_final: 0.7235 (m-40) REVERT: e 128 MET cc_start: 0.7119 (mmm) cc_final: 0.6816 (mmt) REVERT: f 56 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: f 104 LYS cc_start: 0.9213 (mttt) cc_final: 0.8811 (mmmt) REVERT: f 128 MET cc_start: 0.7156 (ttt) cc_final: 0.6655 (mmt) REVERT: f 135 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (mp) REVERT: f 140 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7648 (mp) REVERT: g 65 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7942 (mp) REVERT: m 53 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: m 188 ASP cc_start: 0.8407 (t0) cc_final: 0.8050 (t70) REVERT: m 211 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8744 (t0) REVERT: m 233 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8165 (tt0) REVERT: n 33 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8429 (ttmm) REVERT: n 121 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7020 (tt0) REVERT: n 135 ASP cc_start: 0.8611 (t70) cc_final: 0.8316 (t0) REVERT: n 137 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8549 (mtmm) outliers start: 41 outliers final: 22 residues processed: 169 average time/residue: 0.4780 time to fit residues: 86.3451 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 163 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093432 restraints weight = 11455.261| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.90 r_work: 0.2912 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8532 Z= 0.121 Angle : 0.589 10.200 11584 Z= 0.310 Chirality : 0.042 0.187 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.380 62.563 1208 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.06 % Favored : 93.85 % Rotamer: Outliers : 4.54 % Allowed : 16.95 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.15 (0.26), residues: 1040 helix: 3.64 (0.31), residues: 237 sheet: 0.93 (0.32), residues: 264 loop : -2.61 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 101 TYR 0.017 0.001 TYR b 42 PHE 0.014 0.001 PHE m 55 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8519) covalent geometry : angle 0.58725 (11558) SS BOND : bond 0.00306 ( 13) SS BOND : angle 1.19196 ( 26) hydrogen bonds : bond 0.05106 ( 356) hydrogen bonds : angle 3.80921 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8205 (tppp) cc_final: 0.7330 (tmmm) REVERT: d 29 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7685 (mp) REVERT: d 92 MET cc_start: 0.8542 (mmm) cc_final: 0.7835 (mmm) REVERT: e 85 LYS cc_start: 0.8852 (mttt) cc_final: 0.8623 (mtmt) REVERT: e 103 SER cc_start: 0.8900 (t) cc_final: 0.8634 (m) REVERT: e 104 LYS cc_start: 0.8988 (mtpm) cc_final: 0.8755 (mtmp) REVERT: e 121 ASN cc_start: 0.7824 (m110) cc_final: 0.7220 (m-40) REVERT: e 128 MET cc_start: 0.7000 (mmm) cc_final: 0.6699 (mmt) REVERT: f 56 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: f 104 LYS cc_start: 0.9192 (mttt) cc_final: 0.8814 (mmmt) REVERT: f 128 MET cc_start: 0.7085 (ttt) cc_final: 0.6581 (mmt) REVERT: f 135 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7825 (mp) REVERT: f 140 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7666 (mp) REVERT: g 65 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7945 (mp) REVERT: m 53 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7656 (pt0) REVERT: m 188 ASP cc_start: 0.8249 (t0) cc_final: 0.7898 (t70) REVERT: m 211 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8698 (t0) REVERT: n 33 LYS cc_start: 0.8722 (ttpt) cc_final: 0.8392 (ttmm) REVERT: n 50 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6122 (p90) REVERT: n 121 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6994 (tt0) REVERT: n 123 TYR cc_start: 0.7675 (m-80) cc_final: 0.7402 (m-80) REVERT: n 135 ASP cc_start: 0.8504 (t70) cc_final: 0.8271 (t0) REVERT: n 137 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8428 (mtmm) outliers start: 42 outliers final: 22 residues processed: 169 average time/residue: 0.4749 time to fit residues: 85.6816 Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 163 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093704 restraints weight = 11265.326| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.92 r_work: 0.2914 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8532 Z= 0.119 Angle : 0.599 10.609 11584 Z= 0.311 Chirality : 0.042 0.183 1299 Planarity : 0.004 0.036 1468 Dihedral : 5.247 60.300 1208 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 4.21 % Allowed : 17.28 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.02 (0.26), residues: 1040 helix: 3.82 (0.30), residues: 237 sheet: 1.14 (0.33), residues: 255 loop : -2.53 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f 115 TYR 0.025 0.001 TYR m 93 PHE 0.013 0.001 PHE m 55 TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8519) covalent geometry : angle 0.59648 (11558) SS BOND : bond 0.00286 ( 13) SS BOND : angle 1.27902 ( 26) hydrogen bonds : bond 0.04850 ( 356) hydrogen bonds : angle 3.72194 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8115 (tppp) cc_final: 0.7345 (tmmm) REVERT: d 29 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7701 (mp) REVERT: d 92 MET cc_start: 0.8570 (mmm) cc_final: 0.7954 (mmm) REVERT: e 85 LYS cc_start: 0.8890 (mttt) cc_final: 0.8670 (mtmt) REVERT: e 103 SER cc_start: 0.8909 (t) cc_final: 0.8641 (m) REVERT: e 128 MET cc_start: 0.7013 (mmm) cc_final: 0.6719 (mmt) REVERT: f 56 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: f 104 LYS cc_start: 0.9217 (mttt) cc_final: 0.8872 (mmmt) REVERT: f 128 MET cc_start: 0.7078 (ttt) cc_final: 0.6577 (mmt) REVERT: f 135 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7891 (mp) REVERT: f 140 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7737 (mp) REVERT: m 53 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: m 188 ASP cc_start: 0.8249 (t0) cc_final: 0.7939 (t70) REVERT: m 211 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8710 (t0) REVERT: n 33 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8463 (ttmm) REVERT: n 50 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6286 (p90) REVERT: n 121 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6983 (tt0) REVERT: n 123 TYR cc_start: 0.7813 (m-80) cc_final: 0.7483 (m-80) REVERT: n 135 ASP cc_start: 0.8444 (t70) cc_final: 0.8212 (t0) REVERT: n 137 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8425 (mtmm) outliers start: 39 outliers final: 21 residues processed: 164 average time/residue: 0.5044 time to fit residues: 88.2477 Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN m 211 ASN n 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089957 restraints weight = 11372.665| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.88 r_work: 0.2859 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8532 Z= 0.155 Angle : 0.646 10.854 11584 Z= 0.336 Chirality : 0.044 0.193 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.418 58.722 1208 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.54 % Favored : 93.37 % Rotamer: Outliers : 4.64 % Allowed : 16.74 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.05 (0.26), residues: 1040 helix: 3.78 (0.30), residues: 237 sheet: 1.03 (0.34), residues: 253 loop : -2.52 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 115 TYR 0.017 0.002 TYR b 42 PHE 0.015 0.002 PHE e 110 TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS e 61 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8519) covalent geometry : angle 0.64299 (11558) SS BOND : bond 0.00400 ( 13) SS BOND : angle 1.40329 ( 26) hydrogen bonds : bond 0.06092 ( 356) hydrogen bonds : angle 3.97370 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.298 Fit side-chains REVERT: b 54 LYS cc_start: 0.8105 (tppp) cc_final: 0.7281 (tmmm) REVERT: d 29 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7932 (mp) REVERT: d 92 MET cc_start: 0.8682 (mmm) cc_final: 0.8038 (mmm) REVERT: e 103 SER cc_start: 0.8824 (t) cc_final: 0.8519 (m) REVERT: e 104 LYS cc_start: 0.8989 (mtpm) cc_final: 0.8749 (mtpt) REVERT: e 128 MET cc_start: 0.7347 (mmm) cc_final: 0.7019 (mmt) REVERT: f 56 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: f 104 LYS cc_start: 0.9205 (mttt) cc_final: 0.8741 (mmmt) REVERT: f 128 MET cc_start: 0.7266 (ttt) cc_final: 0.6725 (mmt) REVERT: f 135 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7914 (mp) REVERT: f 140 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7711 (mp) REVERT: m 53 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7750 (pt0) REVERT: m 94 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8314 (pt) REVERT: m 182 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8328 (pt) REVERT: m 188 ASP cc_start: 0.8401 (t0) cc_final: 0.8069 (t70) REVERT: m 211 ASN cc_start: 0.9086 (t0) cc_final: 0.8738 (t0) REVERT: n 33 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8430 (ttmm) REVERT: n 50 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6184 (p90) REVERT: n 121 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7119 (tt0) REVERT: n 135 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8248 (t0) REVERT: n 137 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8489 (mtmm) outliers start: 43 outliers final: 24 residues processed: 165 average time/residue: 0.4642 time to fit residues: 81.9544 Evaluate side-chains 170 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 124 GLU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 135 ASP Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 0.0070 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 0.0470 chunk 96 optimal weight: 1.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094188 restraints weight = 11351.734| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.86 r_work: 0.2925 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8532 Z= 0.116 Angle : 0.599 10.769 11584 Z= 0.312 Chirality : 0.042 0.179 1299 Planarity : 0.003 0.034 1468 Dihedral : 5.164 59.489 1208 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.56 % Allowed : 18.47 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.23 (0.26), residues: 1040 helix: 4.03 (0.30), residues: 237 sheet: 1.14 (0.33), residues: 263 loop : -2.38 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG n 114 TYR 0.012 0.001 TYR g 34 PHE 0.012 0.001 PHE m 55 TRP 0.014 0.001 TRP m 197 HIS 0.002 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8519) covalent geometry : angle 0.59719 (11558) SS BOND : bond 0.00255 ( 13) SS BOND : angle 1.14952 ( 26) hydrogen bonds : bond 0.04685 ( 356) hydrogen bonds : angle 3.73213 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.302 Fit side-chains REVERT: b 54 LYS cc_start: 0.8083 (tppp) cc_final: 0.7269 (tmmm) REVERT: d 29 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7749 (mt) REVERT: d 92 MET cc_start: 0.8741 (mmm) cc_final: 0.8137 (mmm) REVERT: e 39 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8450 (m) REVERT: e 103 SER cc_start: 0.8839 (t) cc_final: 0.8544 (m) REVERT: e 104 LYS cc_start: 0.8953 (mtpm) cc_final: 0.8699 (mtpt) REVERT: e 128 MET cc_start: 0.7108 (mmm) cc_final: 0.6821 (mmt) REVERT: f 56 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: f 104 LYS cc_start: 0.9218 (mttt) cc_final: 0.8841 (mmmt) REVERT: f 128 MET cc_start: 0.7060 (ttt) cc_final: 0.6523 (mmt) REVERT: f 140 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7635 (mp) REVERT: m 53 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: m 188 ASP cc_start: 0.8377 (t0) cc_final: 0.8044 (t70) REVERT: m 211 ASN cc_start: 0.9088 (t0) cc_final: 0.8689 (t0) REVERT: n 33 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8419 (ttmm) REVERT: n 50 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6196 (p90) REVERT: n 98 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7887 (mt) REVERT: n 121 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7110 (tt0) REVERT: n 135 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8190 (t0) REVERT: n 137 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8482 (mtmm) REVERT: n 250 VAL cc_start: 0.8758 (m) cc_final: 0.8492 (t) outliers start: 33 outliers final: 19 residues processed: 166 average time/residue: 0.4873 time to fit residues: 86.2546 Evaluate side-chains 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 124 GLU Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 135 ASP Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091530 restraints weight = 11388.356| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.87 r_work: 0.2882 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8532 Z= 0.139 Angle : 0.642 10.685 11584 Z= 0.330 Chirality : 0.043 0.188 1299 Planarity : 0.004 0.035 1468 Dihedral : 5.286 59.446 1208 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 4.21 % Allowed : 17.82 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.23 (0.26), residues: 1040 helix: 4.06 (0.30), residues: 237 sheet: 1.27 (0.34), residues: 244 loop : -2.35 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.019 0.001 TYR b 42 PHE 0.011 0.001 PHE m 55 TRP 0.012 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8519) covalent geometry : angle 0.63962 (11558) SS BOND : bond 0.00352 ( 13) SS BOND : angle 1.22822 ( 26) hydrogen bonds : bond 0.05459 ( 356) hydrogen bonds : angle 3.85102 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.275 Fit side-chains REVERT: b 54 LYS cc_start: 0.8075 (tppp) cc_final: 0.7252 (tmmm) REVERT: d 29 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7844 (mp) REVERT: d 92 MET cc_start: 0.8695 (mmm) cc_final: 0.8022 (mmm) REVERT: e 103 SER cc_start: 0.8827 (t) cc_final: 0.8533 (m) REVERT: e 104 LYS cc_start: 0.8979 (mtpm) cc_final: 0.8704 (mtpt) REVERT: e 128 MET cc_start: 0.7266 (mmm) cc_final: 0.6957 (mmt) REVERT: f 56 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: f 101 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7724 (ttt180) REVERT: f 104 LYS cc_start: 0.9155 (mttt) cc_final: 0.8749 (mmmt) REVERT: f 128 MET cc_start: 0.7130 (ttt) cc_final: 0.6589 (mmt) REVERT: f 140 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7703 (mp) REVERT: m 53 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: m 113 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7840 (ptt) REVERT: m 188 ASP cc_start: 0.8392 (t0) cc_final: 0.8051 (t70) REVERT: m 211 ASN cc_start: 0.9078 (t0) cc_final: 0.8662 (t0) REVERT: n 33 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8438 (ttmm) REVERT: n 50 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6201 (p90) REVERT: n 98 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7921 (mt) REVERT: n 121 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7126 (tt0) REVERT: n 135 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8203 (t0) REVERT: n 137 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8504 (mtmm) outliers start: 39 outliers final: 21 residues processed: 165 average time/residue: 0.4707 time to fit residues: 83.0799 Evaluate side-chains 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 124 GLU Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 135 ASP Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090877 restraints weight = 11270.753| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.87 r_work: 0.2871 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8532 Z= 0.148 Angle : 0.667 10.900 11584 Z= 0.343 Chirality : 0.043 0.187 1299 Planarity : 0.004 0.037 1468 Dihedral : 5.332 59.523 1208 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 3.56 % Allowed : 18.79 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1040 helix: 4.03 (0.30), residues: 237 sheet: 1.31 (0.34), residues: 254 loop : -2.38 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG n 114 TYR 0.025 0.001 TYR m 93 PHE 0.012 0.001 PHE m 189 TRP 0.012 0.001 TRP m 197 HIS 0.007 0.001 HIS n 48 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8519) covalent geometry : angle 0.66471 (11558) SS BOND : bond 0.00361 ( 13) SS BOND : angle 1.26036 ( 26) hydrogen bonds : bond 0.05784 ( 356) hydrogen bonds : angle 3.89194 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.320 Fit side-chains REVERT: b 54 LYS cc_start: 0.8132 (tppp) cc_final: 0.7260 (tmmm) REVERT: d 29 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7838 (mp) REVERT: d 92 MET cc_start: 0.8712 (mmm) cc_final: 0.8069 (mmm) REVERT: e 103 SER cc_start: 0.8801 (t) cc_final: 0.8483 (m) REVERT: e 104 LYS cc_start: 0.8980 (mtpm) cc_final: 0.8734 (mtmp) REVERT: e 128 MET cc_start: 0.7323 (mmm) cc_final: 0.7001 (mmt) REVERT: f 56 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: f 101 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7754 (ttt180) REVERT: f 104 LYS cc_start: 0.9212 (mttt) cc_final: 0.8778 (mmmt) REVERT: f 128 MET cc_start: 0.7164 (ttt) cc_final: 0.6621 (mmt) REVERT: f 140 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7602 (mp) REVERT: g 65 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7741 (mp) REVERT: m 53 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: m 93 TYR cc_start: 0.7546 (p90) cc_final: 0.7335 (p90) REVERT: m 113 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7892 (ptt) REVERT: m 182 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8345 (pt) REVERT: m 188 ASP cc_start: 0.8420 (t0) cc_final: 0.8051 (t70) REVERT: m 211 ASN cc_start: 0.9069 (t0) cc_final: 0.8646 (t0) REVERT: n 33 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8450 (ttmm) REVERT: n 50 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6258 (p90) REVERT: n 98 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7953 (mt) REVERT: n 121 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7128 (tt0) REVERT: n 135 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8236 (t0) REVERT: n 137 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8508 (mtmm) outliers start: 33 outliers final: 19 residues processed: 159 average time/residue: 0.4699 time to fit residues: 79.9629 Evaluate side-chains 165 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 135 ASP Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 0.0170 chunk 95 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091542 restraints weight = 11267.645| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.86 r_work: 0.2882 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8532 Z= 0.134 Angle : 0.644 10.886 11584 Z= 0.330 Chirality : 0.043 0.187 1299 Planarity : 0.004 0.036 1468 Dihedral : 5.278 59.941 1208 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 3.56 % Allowed : 18.79 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.32 (0.26), residues: 1040 helix: 4.10 (0.30), residues: 237 sheet: 1.34 (0.34), residues: 254 loop : -2.34 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.024 0.001 TYR m 93 PHE 0.011 0.001 PHE m 55 TRP 0.013 0.001 TRP n 259 HIS 0.012 0.001 HIS n 48 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8519) covalent geometry : angle 0.64199 (11558) SS BOND : bond 0.00328 ( 13) SS BOND : angle 1.13066 ( 26) hydrogen bonds : bond 0.05397 ( 356) hydrogen bonds : angle 3.82843 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.82 seconds wall clock time: 53 minutes 54.24 seconds (3234.24 seconds total)