Starting phenix.real_space_refine on Thu Jul 2 11:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fje_31619/07_2026/7fje_31619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fje_31619/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fje_31619/07_2026/7fje_31619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fje_31619/07_2026/7fje_31619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fje_31619/07_2026/7fje_31619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fje_31619/07_2026/7fje_31619.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fje_31619/07_2026/7fje_31619.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fje_31619/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.69, 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: 0.50 Conformation dependent library (CDL) restraints added in 415.5 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: 0.25 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: 1.24 Time building geometry restraints manager: 0.69 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: 4778 16.48 - 32.97: 228 32.97 - 49.45: 83 49.45 - 65.93: 9 65.93 - 82.42: 8 Dihedral angle restraints: 5106 sinusoidal: 2030 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 5103 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 11.565 76.759 3093 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/Z covalent geometry : bond 0.00983 / 0.42 ( 8519) covalent geometry : angle 1.19248 / 0.64 (11558) SS BOND : bond 0.00655 / 0.36 ( 13) SS BOND : angle 2.42578 / 1.75 ( 26) hydrogen bonds : bond 0.26696 / 16.87 ( 356) hydrogen bonds : angle 7.26966 / 5.08 ( 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 : 0.333 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: 0.4263 time to fit residues: 103.0931 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 : 0.215 ------------------------------------------------------------------------------- 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... 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 = 0.3650 r_free = 0.3650 target = 0.135482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093170 restraints weight = 11274.978| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.86 r_work: 0.2921 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8532 Z= 0.153 Angle : 0.703 10.509 11584 Z= 0.367 Chirality : 0.045 0.228 1299 Planarity : 0.005 0.049 1468 Dihedral : 6.135 55.837 1156 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 3.89 % Allowed : 12.53 % Favored : 83.59 % 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: -1.47 (0.24), residues: 1040 helix: 2.00 (0.33), residues: 238 sheet: -0.05 (0.33), residues: 252 loop : -3.00 (0.20), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 91 TYR 0.024 0.002 TYR n 50 PHE 0.018 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/Z covalent geometry : bond 0.00326 / 0.15 ( 8519) covalent geometry : angle 0.69604 / 0.36 (11558) SS BOND : bond 0.00341 / 0.21 ( 13) SS BOND : angle 2.14303 / 1.58 ( 26) hydrogen bonds : bond 0.06816 / 4.37 ( 356) hydrogen bonds : angle 4.54693 / 3.08 ( 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 208 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8157 (tppp) cc_final: 0.7332 (tmmm) REVERT: d 29 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8036 (mt) REVERT: e 39 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8489 (m) REVERT: e 85 LYS cc_start: 0.8789 (mttt) cc_final: 0.8560 (mmmm) REVERT: e 103 SER cc_start: 0.8966 (t) cc_final: 0.8727 (m) REVERT: e 104 LYS cc_start: 0.8932 (mtpm) cc_final: 0.8651 (mtmp) REVERT: e 125 MET cc_start: 0.8739 (tpp) cc_final: 0.8474 (mmm) REVERT: e 128 MET cc_start: 0.7405 (mmm) cc_final: 0.7040 (mmt) REVERT: f 56 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: f 74 ASN cc_start: 0.5681 (OUTLIER) cc_final: 0.5481 (p0) REVERT: f 104 LYS cc_start: 0.9248 (mttt) cc_final: 0.8795 (mmmt) REVERT: g 105 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: m 53 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: m 71 TYR cc_start: 0.7007 (t80) cc_final: 0.5139 (t80) REVERT: m 188 ASP cc_start: 0.8428 (t0) cc_final: 0.8066 (t70) REVERT: m 233 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8223 (tt0) REVERT: n 33 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8114 (tttt) REVERT: n 121 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6723 (mp0) REVERT: n 123 TYR cc_start: 0.7552 (m-80) cc_final: 0.7287 (m-80) REVERT: n 135 ASP cc_start: 0.8680 (t70) cc_final: 0.8397 (t0) outliers start: 36 outliers final: 17 residues processed: 191 average time/residue: 0.4376 time to fit residues: 89.5312 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 74 ASN 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 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: 2.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... f 51 GLN g 52 ASN m 168 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.091747 restraints weight = 11241.922| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.86 r_work: 0.2896 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2798 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= 0.147 Angle : 0.653 10.429 11584 Z= 0.342 Chirality : 0.044 0.214 1299 Planarity : 0.004 0.047 1468 Dihedral : 5.606 57.242 1152 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 4.32 % Allowed : 15.33 % 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: -0.86 (0.25), residues: 1040 helix: 2.78 (0.32), residues: 240 sheet: 0.49 (0.34), residues: 248 loop : -2.85 (0.21), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 115 TYR 0.022 0.002 TYR g 34 PHE 0.015 0.001 PHE e 110 TRP 0.013 0.001 TRP m 197 HIS 0.005 0.001 HIS g 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 8519) covalent geometry : angle 0.64979 / 0.34 (11558) SS BOND : bond 0.00419 / 0.24 ( 13) SS BOND : angle 1.56653 / 1.05 ( 26) hydrogen bonds : bond 0.06338 / 4.07 ( 356) hydrogen bonds : angle 4.22236 / 2.86 ( 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 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8192 (tppp) cc_final: 0.7337 (tmmm) REVERT: d 29 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7958 (mp) REVERT: e 85 LYS cc_start: 0.8871 (mttt) cc_final: 0.8584 (mmmm) REVERT: e 103 SER cc_start: 0.8974 (t) cc_final: 0.8716 (m) REVERT: e 104 LYS cc_start: 0.8950 (mtpm) cc_final: 0.8665 (mtmp) REVERT: e 121 ASN cc_start: 0.7855 (m110) cc_final: 0.7293 (m-40) REVERT: e 125 MET cc_start: 0.8719 (tpp) cc_final: 0.8493 (mmm) REVERT: e 128 MET cc_start: 0.7349 (mmm) cc_final: 0.7015 (mmt) REVERT: f 56 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: f 104 LYS cc_start: 0.9241 (mttt) cc_final: 0.8809 (mmmt) REVERT: f 135 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7919 (mp) REVERT: f 140 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7617 (mp) REVERT: m 47 TYR cc_start: 0.8580 (p90) cc_final: 0.8255 (p90) REVERT: m 53 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: m 71 TYR cc_start: 0.6842 (t80) cc_final: 0.5405 (t80) REVERT: m 188 ASP cc_start: 0.8424 (t0) cc_final: 0.8067 (t70) REVERT: m 211 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8718 (t0) REVERT: m 233 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8161 (tt0) REVERT: n 33 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8417 (ttmm) REVERT: n 121 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6855 (mp0) REVERT: n 123 TYR cc_start: 0.7776 (m-80) cc_final: 0.7419 (m-80) outliers start: 40 outliers final: 22 residues processed: 169 average time/residue: 0.4780 time to fit residues: 86.2478 Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU 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 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 92 ASN 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 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: 2.9990 chunk 73 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 37 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 244 GLN n 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092505 restraints weight = 11442.409| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.93 r_work: 0.2908 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8532 Z= 0.127 Angle : 0.608 10.467 11584 Z= 0.319 Chirality : 0.043 0.203 1299 Planarity : 0.004 0.042 1468 Dihedral : 5.261 57.113 1152 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 4.75 % Allowed : 16.85 % Favored : 78.40 % 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: -0.49 (0.26), residues: 1040 helix: 3.31 (0.32), residues: 239 sheet: 0.68 (0.34), residues: 250 loop : -2.72 (0.21), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 101 TYR 0.028 0.001 TYR m 93 PHE 0.017 0.001 PHE m 55 TRP 0.013 0.001 TRP n 259 HIS 0.004 0.001 HIS g 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8519) covalent geometry : angle 0.60533 / 0.32 (11558) SS BOND : bond 0.00336 / 0.19 ( 13) SS BOND : angle 1.35238 / 0.88 ( 26) hydrogen bonds : bond 0.05446 / 3.50 ( 356) hydrogen bonds : angle 3.95465 / 2.69 ( 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 190 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8207 (tppp) cc_final: 0.7334 (tmmm) REVERT: d 29 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7806 (mp) REVERT: e 85 LYS cc_start: 0.8887 (mttt) cc_final: 0.8560 (mmmm) REVERT: e 103 SER cc_start: 0.8934 (t) cc_final: 0.8688 (m) REVERT: e 121 ASN cc_start: 0.7861 (m110) cc_final: 0.7270 (m-40) REVERT: e 128 MET cc_start: 0.7248 (mmm) cc_final: 0.6941 (mmt) REVERT: f 56 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: f 104 LYS cc_start: 0.9239 (mttt) cc_final: 0.8787 (mmmt) REVERT: f 128 MET cc_start: 0.7163 (ttt) cc_final: 0.6665 (mmt) REVERT: f 135 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (mp) REVERT: f 140 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7649 (mp) REVERT: g 65 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7938 (mp) REVERT: m 53 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: m 188 ASP cc_start: 0.8401 (t0) cc_final: 0.8046 (t70) REVERT: m 211 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8727 (t0) REVERT: m 233 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8206 (tt0) REVERT: n 33 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8460 (ttmm) REVERT: n 113 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7697 (ttp-170) REVERT: n 121 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7056 (tt0) REVERT: n 123 TYR cc_start: 0.7936 (m-80) cc_final: 0.7609 (m-80) outliers start: 44 outliers final: 24 residues processed: 171 average time/residue: 0.4833 time to fit residues: 88.1833 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 82 ARG 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 m residue 267 THR 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 261 ARG Chi-restraints excluded: chain n residue 294 VAL 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: 1.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 0.2980 chunk 82 optimal weight: 0.0870 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093631 restraints weight = 11473.207| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.95 r_work: 0.2907 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8532 Z= 0.118 Angle : 0.593 10.532 11584 Z= 0.310 Chirality : 0.042 0.189 1299 Planarity : 0.004 0.037 1468 Dihedral : 5.091 57.204 1152 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.67 % Favored : 94.13 % Rotamer: Outliers : 4.43 % Allowed : 17.93 % 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: -0.19 (0.26), residues: 1040 helix: 3.66 (0.31), residues: 237 sheet: 0.89 (0.33), residues: 265 loop : -2.65 (0.22), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG m 145 TYR 0.020 0.001 TYR g 34 PHE 0.013 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/Z covalent geometry : bond 0.00251 / 0.12 ( 8519) covalent geometry : angle 0.59098 / 0.31 (11558) SS BOND : bond 0.00299 / 0.17 ( 13) SS BOND : angle 1.15368 / 0.76 ( 26) hydrogen bonds : bond 0.05016 / 3.22 ( 356) hydrogen bonds : angle 3.81281 / 2.59 ( 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: 41 poor density : 142 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8214 (tppp) cc_final: 0.7334 (tmmm) REVERT: d 29 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7659 (mp) REVERT: e 103 SER cc_start: 0.8924 (t) cc_final: 0.8658 (m) REVERT: e 104 LYS cc_start: 0.8940 (mtpm) cc_final: 0.8687 (mtmp) REVERT: e 128 MET cc_start: 0.7012 (mmm) cc_final: 0.6718 (mmt) REVERT: f 56 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: f 104 LYS cc_start: 0.9189 (mttt) cc_final: 0.8809 (mmmt) REVERT: f 128 MET cc_start: 0.7068 (ttt) cc_final: 0.6567 (mmt) REVERT: f 140 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7683 (mp) REVERT: g 51 LYS cc_start: 0.7308 (tppt) cc_final: 0.7000 (tppt) REVERT: g 65 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7912 (mp) REVERT: m 53 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: m 188 ASP cc_start: 0.8248 (t0) cc_final: 0.7925 (t70) REVERT: m 211 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8714 (t0) REVERT: n 33 LYS cc_start: 0.8721 (ttpt) cc_final: 0.8388 (ttmm) REVERT: n 121 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7013 (tt0) REVERT: n 123 TYR cc_start: 0.7912 (m-80) cc_final: 0.7626 (m-80) outliers start: 41 outliers final: 21 residues processed: 168 average time/residue: 0.4859 time to fit residues: 87.1322 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 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 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 261 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.0030 chunk 77 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 121 ASN m 168 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092049 restraints weight = 11307.850| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.86 r_work: 0.2899 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8532 Z= 0.133 Angle : 0.622 10.168 11584 Z= 0.323 Chirality : 0.043 0.194 1299 Planarity : 0.004 0.037 1468 Dihedral : 5.175 61.706 1152 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 5.18 % Allowed : 17.28 % Favored : 77.54 % 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: -0.09 (0.26), residues: 1040 helix: 3.79 (0.31), residues: 237 sheet: 0.98 (0.34), residues: 255 loop : -2.57 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.029 0.001 TYR m 93 PHE 0.013 0.001 PHE m 55 TRP 0.013 0.001 TRP m 197 HIS 0.004 0.001 HIS g 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8519) covalent geometry : angle 0.61898 / 0.32 (11558) SS BOND : bond 0.00351 / 0.20 ( 13) SS BOND : angle 1.42013 / 0.93 ( 26) hydrogen bonds : bond 0.05441 / 3.50 ( 356) hydrogen bonds : angle 3.83080 / 2.61 ( 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 184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8195 (tppp) cc_final: 0.7281 (tmmm) REVERT: d 29 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7833 (mp) REVERT: d 123 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6994 (p90) REVERT: e 103 SER cc_start: 0.8889 (t) cc_final: 0.8594 (m) REVERT: e 104 LYS cc_start: 0.8978 (mtpm) cc_final: 0.8740 (mtmp) REVERT: e 128 MET cc_start: 0.7234 (mmm) cc_final: 0.6924 (mmt) REVERT: f 56 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8021 (mm-30) REVERT: f 104 LYS cc_start: 0.9230 (mttt) cc_final: 0.8768 (mmmt) REVERT: f 128 MET cc_start: 0.7171 (ttt) cc_final: 0.6638 (mmt) REVERT: f 135 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (mp) REVERT: f 140 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7707 (mp) REVERT: g 65 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (mp) REVERT: m 53 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: m 188 ASP cc_start: 0.8397 (t0) cc_final: 0.8038 (t70) REVERT: m 211 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8793 (t0) REVERT: n 33 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8405 (ttmm) REVERT: n 50 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6087 (p90) REVERT: n 121 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7082 (tt0) outliers start: 48 outliers final: 24 residues processed: 168 average time/residue: 0.4987 time to fit residues: 89.6420 Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 m residue 267 THR 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 137 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 51 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 61 HIS e 121 ASN g 29 HIS ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096803 restraints weight = 11480.095| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.90 r_work: 0.2978 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8532 Z= 0.103 Angle : 0.567 10.849 11584 Z= 0.295 Chirality : 0.041 0.178 1299 Planarity : 0.003 0.033 1468 Dihedral : 4.838 60.518 1152 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 3.56 % Allowed : 18.90 % Favored : 77.54 % 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: 0.22 (0.26), residues: 1040 helix: 4.04 (0.30), residues: 237 sheet: 1.15 (0.33), residues: 257 loop : -2.36 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG m 99 TYR 0.029 0.001 TYR m 93 PHE 0.013 0.001 PHE m 55 TRP 0.013 0.001 TRP n 259 HIS 0.002 0.001 HIS g 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 8519) covalent geometry : angle 0.56615 / 0.29 (11558) SS BOND : bond 0.00195 / 0.11 ( 13) SS BOND : angle 0.84829 / 0.54 ( 26) hydrogen bonds : bond 0.03887 / 2.52 ( 356) hydrogen bonds : angle 3.52836 / 2.42 ( 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 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8076 (tppp) cc_final: 0.7282 (tmmm) REVERT: e 39 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8359 (m) REVERT: e 103 SER cc_start: 0.8876 (t) cc_final: 0.8601 (m) REVERT: e 104 LYS cc_start: 0.8930 (mtpm) cc_final: 0.8708 (mtmp) REVERT: e 128 MET cc_start: 0.6887 (mmm) cc_final: 0.6604 (mmt) REVERT: f 56 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: f 101 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7708 (ttt180) REVERT: f 104 LYS cc_start: 0.9188 (mttt) cc_final: 0.8812 (mmmt) REVERT: f 128 MET cc_start: 0.7057 (ttt) cc_final: 0.6518 (mmt) REVERT: f 140 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7605 (mp) REVERT: g 131 VAL cc_start: 0.8342 (t) cc_final: 0.8120 (t) REVERT: g 135 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6652 (t80) REVERT: m 53 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: m 188 ASP cc_start: 0.8354 (t0) cc_final: 0.8018 (t70) REVERT: m 211 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8772 (t0) REVERT: n 33 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8393 (ttmm) REVERT: n 50 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6127 (p90) REVERT: n 98 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7872 (mt) REVERT: n 121 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7077 (tt0) REVERT: n 123 TYR cc_start: 0.7794 (m-80) cc_final: 0.7506 (m-80) REVERT: n 250 VAL cc_start: 0.8714 (m) cc_final: 0.8396 (t) outliers start: 33 outliers final: 15 residues processed: 174 average time/residue: 0.4467 time to fit residues: 83.1767 Evaluate side-chains 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 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 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 80 ASP Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 211 ASN 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 261 ARG Chi-restraints excluded: chain n residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 68 optimal weight: 0.0370 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 121 ASN m 163 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.094319 restraints weight = 11368.907| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.89 r_work: 0.2924 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8532 Z= 0.119 Angle : 0.614 10.906 11584 Z= 0.313 Chirality : 0.042 0.184 1299 Planarity : 0.003 0.033 1468 Dihedral : 4.944 60.405 1152 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.35 % Allowed : 19.55 % Favored : 77.11 % 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: 0.31 (0.26), residues: 1040 helix: 4.12 (0.30), residues: 237 sheet: 1.20 (0.33), residues: 257 loop : -2.31 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG m 99 TYR 0.028 0.001 TYR m 93 PHE 0.014 0.001 PHE g 64 TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8519) covalent geometry : angle 0.61286 / 0.31 (11558) SS BOND : bond 0.00275 / 0.16 ( 13) SS BOND : angle 1.10372 / 0.71 ( 26) hydrogen bonds : bond 0.04473 / 2.89 ( 356) hydrogen bonds : angle 3.63559 / 2.49 ( 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 169 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8052 (tppp) cc_final: 0.7287 (tmmm) REVERT: e 103 SER cc_start: 0.8888 (t) cc_final: 0.8616 (m) REVERT: e 104 LYS cc_start: 0.8999 (mtpm) cc_final: 0.8732 (mtmp) REVERT: e 128 MET cc_start: 0.6933 (mmm) cc_final: 0.6656 (mmt) REVERT: f 56 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: f 101 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7897 (ttt180) REVERT: f 104 LYS cc_start: 0.9166 (mttt) cc_final: 0.8834 (mmmt) REVERT: f 128 MET cc_start: 0.7013 (ttt) cc_final: 0.6456 (mmt) REVERT: f 140 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7743 (mp) REVERT: m 53 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: m 188 ASP cc_start: 0.8253 (t0) cc_final: 0.7927 (t70) REVERT: m 211 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8700 (t0) REVERT: n 33 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8492 (ttmm) REVERT: n 50 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6036 (p90) REVERT: n 98 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7918 (mt) REVERT: n 121 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7132 (tt0) outliers start: 31 outliers final: 15 residues processed: 159 average time/residue: 0.4586 time to fit residues: 78.0295 Evaluate side-chains 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 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 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 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 261 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.135239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092516 restraints weight = 11391.945| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.88 r_work: 0.2896 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8532 Z= 0.130 Angle : 0.635 10.519 11584 Z= 0.326 Chirality : 0.042 0.178 1299 Planarity : 0.004 0.034 1468 Dihedral : 5.041 60.591 1152 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 3.56 % Allowed : 19.55 % Favored : 76.89 % 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: 0.29 (0.26), residues: 1040 helix: 4.11 (0.30), residues: 237 sheet: 1.14 (0.34), residues: 246 loop : -2.23 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.028 0.001 TYR m 93 PHE 0.011 0.001 PHE m 55 TRP 0.011 0.001 TRP m 197 HIS 0.003 0.001 HIS n 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8519) covalent geometry : angle 0.63275 / 0.32 (11558) SS BOND : bond 0.00327 / 0.19 ( 13) SS BOND : angle 1.20855 / 0.79 ( 26) hydrogen bonds : bond 0.05148 / 3.33 ( 356) hydrogen bonds : angle 3.72781 / 2.54 ( 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 170 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8067 (tppp) cc_final: 0.7257 (tmmm) REVERT: d 29 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7821 (mp) REVERT: e 103 SER cc_start: 0.8809 (t) cc_final: 0.8486 (m) REVERT: e 104 LYS cc_start: 0.8968 (mtpm) cc_final: 0.8733 (mtmp) REVERT: e 128 MET cc_start: 0.7195 (mmm) cc_final: 0.6904 (mmt) REVERT: f 56 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8068 (mm-30) REVERT: f 104 LYS cc_start: 0.9113 (mttt) cc_final: 0.8734 (mmmt) REVERT: f 128 MET cc_start: 0.7118 (ttt) cc_final: 0.6529 (mmt) REVERT: f 140 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7703 (mp) REVERT: g 51 LYS cc_start: 0.6768 (tppt) cc_final: 0.6424 (tppt) REVERT: m 53 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: m 113 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7794 (ptt) REVERT: m 188 ASP cc_start: 0.8391 (t0) cc_final: 0.8046 (t70) REVERT: m 211 ASN cc_start: 0.9066 (t0) cc_final: 0.8700 (t0) REVERT: n 25 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8700 (mt0) REVERT: n 33 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8416 (ttmm) REVERT: n 50 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.5980 (p90) REVERT: n 98 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7932 (mt) REVERT: n 121 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7212 (tt0) outliers start: 33 outliers final: 19 residues processed: 159 average time/residue: 0.5079 time to fit residues: 86.3906 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain g residue 30 LEU 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 n residue 25 GLN 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 261 ARG Chi-restraints excluded: chain n residue 295 LEU 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: 10.0000 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.133593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.090812 restraints weight = 11291.819| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.84 r_work: 0.2867 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3638 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= 0.158 Angle : 0.671 10.873 11584 Z= 0.345 Chirality : 0.044 0.191 1299 Planarity : 0.004 0.040 1468 Dihedral : 5.221 58.581 1152 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 3.24 % Allowed : 19.76 % Favored : 77.00 % 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: 0.25 (0.26), residues: 1040 helix: 4.02 (0.30), residues: 237 sheet: 1.26 (0.34), residues: 256 loop : -2.37 (0.22), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 115 TYR 0.029 0.002 TYR m 93 PHE 0.014 0.002 PHE e 110 TRP 0.012 0.001 TRP m 271 HIS 0.004 0.001 HIS n 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8519) covalent geometry : angle 0.66904 / 0.34 (11558) SS BOND : bond 0.00399 / 0.23 ( 13) SS BOND : angle 1.36165 / 0.91 ( 26) hydrogen bonds : bond 0.06048 / 3.90 ( 356) hydrogen bonds : angle 3.89354 / 2.65 ( 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 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8086 (tppp) cc_final: 0.7250 (tmmm) REVERT: d 29 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (mp) REVERT: d 92 MET cc_start: 0.8576 (mmm) cc_final: 0.8113 (mmm) REVERT: e 103 SER cc_start: 0.8807 (t) cc_final: 0.8473 (m) REVERT: e 104 LYS cc_start: 0.8988 (mtpm) cc_final: 0.8738 (mtmp) REVERT: e 128 MET cc_start: 0.7335 (mmm) cc_final: 0.7008 (mmt) REVERT: f 56 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: f 101 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7789 (ttt180) REVERT: f 104 LYS cc_start: 0.9184 (mttt) cc_final: 0.8726 (mmmt) REVERT: f 128 MET cc_start: 0.7200 (ttt) cc_final: 0.6623 (mmt) REVERT: f 140 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7660 (mp) REVERT: m 53 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: m 113 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7853 (ptt) REVERT: m 188 ASP cc_start: 0.8400 (t0) cc_final: 0.8058 (t70) REVERT: m 211 ASN cc_start: 0.9099 (t0) cc_final: 0.8686 (t0) REVERT: n 33 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8454 (ttmm) REVERT: n 50 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6090 (p90) REVERT: n 98 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7966 (mt) REVERT: n 121 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7205 (tt0) outliers start: 30 outliers final: 21 residues processed: 159 average time/residue: 0.5171 time to fit residues: 87.8997 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 : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a 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 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 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 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 137 LYS 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 295 LEU 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: 0.7980 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3634 r_free = 0.3634 target = 0.134915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092280 restraints weight = 11211.387| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.89 r_work: 0.2904 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8532 Z= 0.126 Angle : 0.630 10.724 11584 Z= 0.322 Chirality : 0.042 0.180 1299 Planarity : 0.003 0.034 1468 Dihedral : 5.097 60.311 1152 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 3.24 % Allowed : 20.19 % Favored : 76.57 % 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: 4.12 (0.30), residues: 237 sheet: 1.19 (0.33), residues: 258 loop : -2.23 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG f 115 TYR 0.028 0.001 TYR m 93 PHE 0.011 0.001 PHE m 55 TRP 0.013 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8519) covalent geometry : angle 0.62892 / 0.32 (11558) SS BOND : bond 0.00287 / 0.16 ( 13) SS BOND : angle 1.06237 / 0.70 ( 26) hydrogen bonds : bond 0.05041 / 3.26 ( 356) hydrogen bonds : angle 3.72688 / 2.55 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.35 seconds wall clock time: 53 minutes 50.72 seconds (3230.72 seconds total)