Starting phenix.real_space_refine on Thu Mar 13 01:26:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fje_31619/03_2025/7fje_31619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fje_31619/03_2025/7fje_31619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2025/7fje_31619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2025/7fje_31619.map" model { file = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2025/7fje_31619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fje_31619/03_2025/7fje_31619.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'ASP: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: 5.71, per 1000 atoms: 0.68 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: 2.10 Conformation dependent library (CDL) restraints added in 996.7 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: 1.10 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: 2.51 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2553 1.34 - 1.47: 2224 1.47 - 1.60: 3666 1.60 - 1.73: 0 1.73 - 1.86: 76 Bond restraints: 8519 Sorted by residual: bond pdb=" CA TYR d 79 " pdb=" C TYR d 79 " ideal model delta sigma weight residual 1.523 1.586 -0.063 1.34e-02 5.57e+03 2.20e+01 bond pdb=" C SER e 103 " pdb=" N LYS e 104 " ideal model delta sigma weight residual 1.327 1.233 0.094 2.86e-02 1.22e+03 1.09e+01 bond pdb=" CA SER m 235 " pdb=" CB SER m 235 " ideal model delta sigma weight residual 1.531 1.434 0.097 3.12e-02 1.03e+03 9.61e+00 bond pdb=" CG LEU f 114 " pdb=" CD2 LEU f 114 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB ARG n 228 " pdb=" CG ARG n 228 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 ... (remaining 8514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 11309 3.26 - 6.53: 211 6.53 - 9.79: 29 9.79 - 13.05: 6 13.05 - 16.31: 3 Bond angle restraints: 11558 Sorted by residual: angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.08 -15.74 2.08e+00 2.31e-01 5.73e+01 angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" CA TYR d 79 " pdb=" C TYR d 79 " pdb=" O TYR d 79 " ideal model delta sigma weight residual 120.51 113.15 7.36 1.43e+00 4.89e-01 2.65e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.21 -12.41 2.44e+00 1.68e-01 2.59e+01 angle pdb=" C GLU g 67 " pdb=" N ASP g 68 " pdb=" CA ASP g 68 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 11553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4828 16.48 - 32.97: 228 32.97 - 49.45: 89 49.45 - 65.93: 9 65.93 - 82.42: 8 Dihedral angle restraints: 5162 sinusoidal: 2086 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.66 52.34 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -131.28 -48.72 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1071 0.086 - 0.173: 212 0.173 - 0.259: 13 0.259 - 0.346: 2 0.346 - 0.432: 1 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CG LEU a 27 " pdb=" CB LEU a 27 " pdb=" CD1 LEU a 27 " pdb=" CD2 LEU a 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1296 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.019 2.00e-02 2.50e+03 2.10e-02 8.85e+00 pdb=" CG TYR e 111 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.021 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR d 90 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN n 194 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO n 195 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO n 195 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO n 195 " 0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2178 2.81 - 3.33: 6444 3.33 - 3.85: 12226 3.85 - 4.38: 13205 4.38 - 4.90: 24282 Nonbonded interactions: 58335 Sorted by model distance: nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.287 3.040 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.391 3.120 nonbonded pdb=" OG SER a 23 " pdb=" OE1 GLN d 94 " model vdw 2.405 3.040 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.441 3.120 nonbonded pdb=" O PHE a 24 " pdb=" OG1 THR m 238 " model vdw 2.451 3.040 ... (remaining 58330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 26 through 54) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 155)) selection = (chain 'f' and resid 33 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 8519 Z= 0.643 Angle : 1.192 16.314 11558 Z= 0.641 Chirality : 0.066 0.432 1299 Planarity : 0.008 0.060 1468 Dihedral : 11.624 76.759 3149 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.97 % Allowed : 5.62 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.004 TRP m 197 HIS 0.016 0.004 HIS f 61 PHE 0.036 0.004 PHE n 29 TYR 0.051 0.005 TYR e 111 ARG 0.010 0.001 ARG e 117 *********************** 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 : 1.019 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: 1.0821 time to fit residues: 262.1242 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 : 0.942 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 ASN f 65 ASN f 74 ASN f 121 ASN g 29 HIS g 37 GLN m 86 GLN n 25 GLN n 47 ASN n 221 GLN n 230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093833 restraints weight = 11251.714| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.92 r_work: 0.2915 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8519 Z= 0.192 Angle : 0.685 10.490 11558 Z= 0.359 Chirality : 0.044 0.223 1299 Planarity : 0.005 0.049 1468 Dihedral : 6.570 59.633 1212 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 3.56 % Allowed : 12.74 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1040 helix: 1.99 (0.33), residues: 239 sheet: -0.04 (0.33), residues: 252 loop : -2.99 (0.20), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.004 0.001 HIS g 29 PHE 0.019 0.002 PHE m 157 TYR 0.023 0.002 TYR g 34 ARG 0.004 0.000 ARG d 91 *********************** 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 207 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8152 (tppp) cc_final: 0.7334 (tmmm) REVERT: d 29 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7965 (mp) REVERT: e 37 LYS cc_start: 0.8237 (mmtp) cc_final: 0.8033 (mttm) REVERT: e 85 LYS cc_start: 0.8783 (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: 0.8912 (mtpm) cc_final: 0.8665 (mttp) REVERT: e 125 MET cc_start: 0.8735 (tpp) cc_final: 0.8450 (mmm) REVERT: e 128 MET cc_start: 0.7370 (mmm) cc_final: 0.7021 (mmt) REVERT: f 56 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: f 104 LYS cc_start: 0.9233 (mttt) cc_final: 0.8808 (mmmt) REVERT: g 105 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7277 (tp-100) REVERT: m 53 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: m 71 TYR cc_start: 0.7000 (t80) cc_final: 0.5203 (t80) REVERT: m 188 ASP cc_start: 0.8399 (t0) cc_final: 0.8038 (t70) REVERT: m 233 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8216 (tt0) REVERT: n 33 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8100 (tttt) REVERT: n 121 GLU cc_start: 0.7704 (mt-10) cc_final: 0.6809 (mp0) REVERT: n 123 TYR cc_start: 0.7536 (m-80) cc_final: 0.7268 (m-80) REVERT: n 135 ASP cc_start: 0.8684 (t70) cc_final: 0.8400 (t0) outliers start: 33 outliers final: 16 residues processed: 190 average time/residue: 1.2124 time to fit residues: 246.8294 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 90 SER Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 105 GLN Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 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 245 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 51 GLN f 74 ASN g 37 GLN g 52 ASN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093774 restraints weight = 11345.454| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.93 r_work: 0.2914 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8519 Z= 0.173 Angle : 0.616 9.739 11558 Z= 0.324 Chirality : 0.043 0.206 1299 Planarity : 0.004 0.043 1468 Dihedral : 5.855 63.107 1208 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.15 % Favored : 93.65 % Rotamer: Outliers : 4.54 % Allowed : 14.90 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1040 helix: 2.91 (0.32), residues: 240 sheet: 0.40 (0.33), residues: 254 loop : -2.78 (0.21), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS g 29 PHE 0.013 0.001 PHE m 157 TYR 0.020 0.002 TYR g 34 ARG 0.002 0.000 ARG m 145 *********************** 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 186 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8252 (tppp) cc_final: 0.7431 (tmmm) REVERT: d 29 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7764 (mp) REVERT: e 85 LYS cc_start: 0.8860 (mttt) cc_final: 0.8596 (mmmm) REVERT: e 103 SER cc_start: 0.8968 (t) cc_final: 0.8747 (m) REVERT: e 104 LYS cc_start: 0.8970 (mtpm) cc_final: 0.8729 (mtpp) REVERT: e 120 GLU cc_start: 0.7894 (tp30) cc_final: 0.7673 (tp30) REVERT: e 121 ASN cc_start: 0.7966 (m110) cc_final: 0.7288 (m-40) REVERT: e 128 MET cc_start: 0.7069 (mmm) cc_final: 0.6734 (mmt) REVERT: f 56 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: f 104 LYS cc_start: 0.9205 (mttt) cc_final: 0.8844 (mmmt) REVERT: f 135 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (mp) REVERT: f 140 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7716 (mp) REVERT: m 47 TYR cc_start: 0.8527 (p90) cc_final: 0.8206 (p90) REVERT: m 53 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: m 188 ASP cc_start: 0.8275 (t0) cc_final: 0.7927 (t70) REVERT: m 211 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8666 (t0) REVERT: n 33 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8415 (ttmm) REVERT: n 121 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6977 (tt0) REVERT: n 123 TYR cc_start: 0.7764 (m-80) cc_final: 0.7473 (m-80) outliers start: 42 outliers final: 19 residues processed: 171 average time/residue: 1.1415 time to fit residues: 208.2667 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.0000 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092974 restraints weight = 11269.765| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.92 r_work: 0.2905 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8519 Z= 0.172 Angle : 0.599 10.190 11558 Z= 0.315 Chirality : 0.042 0.199 1299 Planarity : 0.004 0.040 1468 Dihedral : 5.513 58.737 1208 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.58 % Favored : 94.23 % Rotamer: Outliers : 4.43 % Allowed : 16.85 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 1040 helix: 3.46 (0.31), residues: 237 sheet: 0.68 (0.34), residues: 250 loop : -2.66 (0.21), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.002 0.001 HIS n 226 PHE 0.018 0.001 PHE m 55 TYR 0.028 0.001 TYR m 93 ARG 0.003 0.000 ARG f 101 *********************** 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 184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8220 (tppp) cc_final: 0.7356 (tmmm) REVERT: d 29 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7726 (mp) REVERT: e 85 LYS cc_start: 0.8877 (mttt) cc_final: 0.8571 (mmmm) REVERT: e 103 SER cc_start: 0.8946 (t) cc_final: 0.8681 (m) REVERT: e 104 LYS cc_start: 0.8950 (mtpm) cc_final: 0.8696 (mtmp) REVERT: e 128 MET cc_start: 0.7040 (mmm) cc_final: 0.6732 (mmt) REVERT: f 56 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: f 104 LYS cc_start: 0.9199 (mttt) cc_final: 0.8828 (mmmt) REVERT: f 128 MET cc_start: 0.7125 (ttt) cc_final: 0.6635 (mmt) REVERT: f 135 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7871 (mp) REVERT: f 140 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7692 (mp) REVERT: g 65 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8005 (mp) REVERT: m 53 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: m 188 ASP cc_start: 0.8256 (t0) cc_final: 0.7910 (t70) REVERT: m 211 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8670 (t0) REVERT: n 33 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8444 (ttmm) REVERT: n 121 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6974 (tt0) outliers start: 41 outliers final: 22 residues processed: 168 average time/residue: 1.0996 time to fit residues: 197.8826 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 90 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 163 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN n 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092549 restraints weight = 11159.645| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.89 r_work: 0.2895 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8519 Z= 0.177 Angle : 0.599 10.515 11558 Z= 0.315 Chirality : 0.043 0.198 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.370 58.549 1208 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 4.97 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1040 helix: 3.66 (0.31), residues: 237 sheet: 0.84 (0.33), residues: 256 loop : -2.59 (0.22), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS n 226 PHE 0.014 0.001 PHE m 55 TYR 0.020 0.001 TYR g 34 ARG 0.003 0.000 ARG f 115 *********************** 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 187 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8083 (tppp) cc_final: 0.7337 (tmmm) REVERT: d 29 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7711 (mp) REVERT: e 85 LYS cc_start: 0.8903 (mttt) cc_final: 0.8689 (mtmt) REVERT: e 103 SER cc_start: 0.8927 (t) cc_final: 0.8635 (m) REVERT: e 104 LYS cc_start: 0.9007 (mtpm) cc_final: 0.8767 (mtmp) REVERT: e 128 MET cc_start: 0.7095 (mmm) cc_final: 0.6784 (mmt) REVERT: f 56 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: f 104 LYS cc_start: 0.9178 (mttt) cc_final: 0.8813 (mmmt) REVERT: f 128 MET cc_start: 0.7157 (ttt) cc_final: 0.6640 (mmt) REVERT: f 135 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7890 (mp) REVERT: f 140 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7703 (mp) REVERT: g 51 LYS cc_start: 0.7311 (tppt) cc_final: 0.7053 (tppt) REVERT: g 65 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7953 (mp) REVERT: m 53 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: m 94 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8313 (pt) REVERT: m 188 ASP cc_start: 0.8248 (t0) cc_final: 0.7913 (t70) REVERT: m 211 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8674 (t0) REVERT: n 33 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8436 (ttmm) REVERT: n 121 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7049 (tt0) outliers start: 46 outliers final: 24 residues processed: 170 average time/residue: 1.0497 time to fit residues: 191.3205 Evaluate side-chains 169 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain 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 g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 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 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 294 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 61 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095879 restraints weight = 11301.172| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.87 r_work: 0.2967 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8519 Z= 0.141 Angle : 0.575 10.694 11558 Z= 0.300 Chirality : 0.041 0.193 1299 Planarity : 0.003 0.035 1468 Dihedral : 5.062 57.017 1208 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.71 % Rotamer: Outliers : 4.86 % Allowed : 17.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1040 helix: 3.92 (0.31), residues: 237 sheet: 0.98 (0.32), residues: 271 loop : -2.49 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP m 197 HIS 0.003 0.001 HIS n 48 PHE 0.014 0.001 PHE m 55 TYR 0.030 0.001 TYR m 93 ARG 0.002 0.000 ARG m 145 *********************** 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 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8082 (tppp) cc_final: 0.7322 (tmmm) REVERT: d 29 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7669 (mt) REVERT: e 85 LYS cc_start: 0.8892 (mttt) cc_final: 0.8661 (mtmt) REVERT: e 103 SER cc_start: 0.8901 (t) cc_final: 0.8620 (m) REVERT: e 128 MET cc_start: 0.6957 (mmm) cc_final: 0.6657 (mmt) REVERT: f 56 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: f 104 LYS cc_start: 0.9162 (mttt) cc_final: 0.8782 (mmmt) REVERT: f 128 MET cc_start: 0.7079 (ttt) cc_final: 0.6549 (mmt) REVERT: f 140 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7709 (mp) REVERT: g 135 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6707 (t80) REVERT: m 53 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: m 182 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8283 (tt) REVERT: m 188 ASP cc_start: 0.8343 (t0) cc_final: 0.8006 (t70) REVERT: m 211 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8793 (t0) REVERT: n 33 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8371 (ttmm) REVERT: n 50 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6395 (p90) REVERT: n 121 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7100 (tt0) outliers start: 45 outliers final: 17 residues processed: 176 average time/residue: 1.0899 time to fit residues: 205.1323 Evaluate side-chains 165 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 124 GLU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 136 VAL 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 m residue 182 LEU 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 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 215 VAL Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0270 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.0040 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 36 optimal weight: 0.0040 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN ** m 211 ASN ** 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 = 0.3686 r_free = 0.3686 target = 0.139144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097209 restraints weight = 11290.306| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.88 r_work: 0.2962 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8519 Z= 0.144 Angle : 0.580 10.674 11558 Z= 0.298 Chirality : 0.041 0.180 1299 Planarity : 0.003 0.033 1468 Dihedral : 4.949 58.128 1208 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 3.67 % Allowed : 19.01 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1040 helix: 4.09 (0.30), residues: 237 sheet: 1.02 (0.32), residues: 273 loop : -2.39 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.002 0.001 HIS n 48 PHE 0.012 0.001 PHE m 55 TYR 0.028 0.001 TYR m 93 ARG 0.002 0.000 ARG m 99 *********************** 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 180 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.975 Fit side-chains REVERT: b 54 LYS cc_start: 0.8034 (tppp) cc_final: 0.7286 (tmmm) REVERT: d 29 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7681 (mt) REVERT: e 85 LYS cc_start: 0.8877 (mttt) cc_final: 0.8652 (mtmt) REVERT: e 103 SER cc_start: 0.8859 (t) cc_final: 0.8574 (m) REVERT: e 104 LYS cc_start: 0.8990 (mtpm) cc_final: 0.8698 (mtpt) REVERT: e 128 MET cc_start: 0.6811 (mmm) cc_final: 0.6493 (mmt) REVERT: f 56 GLU cc_start: 0.8339 (tp30) cc_final: 0.8015 (mm-30) REVERT: f 104 LYS cc_start: 0.9151 (mttt) cc_final: 0.8827 (mmmt) REVERT: f 109 ASN cc_start: 0.8157 (m-40) cc_final: 0.7564 (m-40) REVERT: f 128 MET cc_start: 0.7062 (ttt) cc_final: 0.6528 (mmt) REVERT: f 140 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7734 (mp) REVERT: g 131 VAL cc_start: 0.8315 (t) cc_final: 0.8101 (t) REVERT: g 135 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6578 (t80) REVERT: m 53 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: m 188 ASP cc_start: 0.8197 (t0) cc_final: 0.7872 (t70) REVERT: m 211 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8661 (t0) REVERT: n 33 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8450 (ttmm) REVERT: n 50 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6401 (p90) REVERT: n 98 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7890 (mt) REVERT: n 121 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7048 (tt0) outliers start: 34 outliers final: 19 residues processed: 169 average time/residue: 1.0484 time to fit residues: 190.8757 Evaluate side-chains 165 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain 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 114 LEU Chi-restraints excluded: chain f residue 124 GLU Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 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 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 79 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 51 optimal weight: 5.9990 chunk 67 optimal weight: 0.0000 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN m 168 GLN m 211 ASN n 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095266 restraints weight = 11244.792| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.82 r_work: 0.2959 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8519 Z= 0.159 Angle : 0.603 10.727 11558 Z= 0.310 Chirality : 0.042 0.182 1299 Planarity : 0.003 0.032 1468 Dihedral : 4.954 57.235 1208 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.71 % Favored : 95.10 % Rotamer: Outliers : 3.67 % Allowed : 19.11 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1040 helix: 4.16 (0.30), residues: 237 sheet: 1.28 (0.32), residues: 274 loop : -2.36 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.008 0.001 HIS n 48 PHE 0.013 0.001 PHE g 64 TYR 0.029 0.001 TYR m 93 ARG 0.007 0.000 ARG n 114 *********************** 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 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.896 Fit side-chains REVERT: b 54 LYS cc_start: 0.8033 (tppp) cc_final: 0.7254 (tmmm) REVERT: d 29 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7634 (mt) REVERT: e 85 LYS cc_start: 0.8870 (mttt) cc_final: 0.8641 (mtmt) REVERT: e 103 SER cc_start: 0.8846 (t) cc_final: 0.8556 (m) REVERT: e 104 LYS cc_start: 0.8949 (mtpm) cc_final: 0.8686 (mtpt) REVERT: e 128 MET cc_start: 0.6984 (mmm) cc_final: 0.6653 (mmt) REVERT: f 56 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: f 104 LYS cc_start: 0.9178 (mttt) cc_final: 0.8825 (mmmt) REVERT: f 109 ASN cc_start: 0.8296 (m-40) cc_final: 0.7732 (m-40) REVERT: f 123 MET cc_start: 0.7980 (ttm) cc_final: 0.7561 (ttt) REVERT: f 128 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6584 (mmt) REVERT: f 140 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7724 (mp) REVERT: g 131 VAL cc_start: 0.8451 (t) cc_final: 0.8226 (t) REVERT: g 135 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6675 (t80) REVERT: m 53 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: m 70 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7599 (mmm) REVERT: m 188 ASP cc_start: 0.8393 (t0) cc_final: 0.8035 (t70) REVERT: m 211 ASN cc_start: 0.9035 (t0) cc_final: 0.8740 (t0) REVERT: n 25 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: n 33 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8512 (ttmm) REVERT: n 50 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6470 (p90) REVERT: n 98 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7908 (mt) REVERT: n 121 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7116 (tt0) REVERT: n 252 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (pm20) outliers start: 34 outliers final: 19 residues processed: 160 average time/residue: 1.0433 time to fit residues: 178.8389 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 : 0.887 ------------------------------------------------------------------------------- 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 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 128 MET 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 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 70 MET 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 137 LYS 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 252 GLN 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 14 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091810 restraints weight = 11393.792| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.84 r_work: 0.2886 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8519 Z= 0.220 Angle : 0.659 10.898 11558 Z= 0.340 Chirality : 0.044 0.187 1299 Planarity : 0.004 0.036 1468 Dihedral : 5.217 56.854 1208 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.77 % Favored : 94.04 % Rotamer: Outliers : 3.78 % Allowed : 19.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1040 helix: 4.11 (0.30), residues: 237 sheet: 1.33 (0.34), residues: 254 loop : -2.38 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 271 HIS 0.008 0.001 HIS n 48 PHE 0.014 0.002 PHE e 110 TYR 0.029 0.002 TYR m 93 ARG 0.006 0.001 ARG n 114 *********************** 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 172 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.053 Fit side-chains REVERT: b 54 LYS cc_start: 0.8073 (tppp) cc_final: 0.7269 (tmmm) REVERT: d 29 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7854 (mp) REVERT: e 103 SER cc_start: 0.8830 (t) cc_final: 0.8496 (m) REVERT: e 104 LYS cc_start: 0.9004 (mtpm) cc_final: 0.8717 (mtpt) REVERT: e 128 MET cc_start: 0.7299 (mmm) cc_final: 0.6973 (mmt) REVERT: f 56 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: f 101 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7779 (ttt180) REVERT: f 104 LYS cc_start: 0.9128 (mttt) cc_final: 0.8744 (mmmt) REVERT: f 128 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6653 (mmt) REVERT: f 135 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7958 (mp) REVERT: f 140 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7727 (mp) REVERT: m 53 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: m 94 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8336 (pt) REVERT: m 188 ASP cc_start: 0.8412 (t0) cc_final: 0.8035 (t70) REVERT: m 211 ASN cc_start: 0.9073 (t0) cc_final: 0.8662 (t0) REVERT: n 25 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8781 (mt0) REVERT: n 33 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8440 (ttmm) REVERT: n 50 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6492 (p90) REVERT: n 98 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7933 (mt) REVERT: n 121 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7117 (tt0) REVERT: n 252 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8598 (pm20) outliers start: 35 outliers final: 19 residues processed: 155 average time/residue: 1.2449 time to fit residues: 205.7126 Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU 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 128 MET Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain 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 137 LYS 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 252 GLN Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093866 restraints weight = 11393.549| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.85 r_work: 0.2909 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8519 Z= 0.176 Angle : 0.627 11.462 11558 Z= 0.323 Chirality : 0.042 0.187 1299 Planarity : 0.004 0.037 1468 Dihedral : 5.134 57.899 1208 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 3.35 % Allowed : 19.87 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 1040 helix: 4.18 (0.30), residues: 237 sheet: 1.36 (0.33), residues: 264 loop : -2.32 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.011 0.001 HIS n 48 PHE 0.011 0.001 PHE m 55 TYR 0.028 0.001 TYR m 93 ARG 0.004 0.000 ARG n 114 ********************** 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 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.012 Fit side-chains REVERT: b 54 LYS cc_start: 0.8044 (tppp) cc_final: 0.7228 (tmmm) REVERT: d 29 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7769 (mp) REVERT: e 103 SER cc_start: 0.8826 (t) cc_final: 0.8499 (m) REVERT: e 104 LYS cc_start: 0.8981 (mtpm) cc_final: 0.8708 (mtpt) REVERT: e 128 MET cc_start: 0.7229 (mmm) cc_final: 0.6912 (mmt) REVERT: f 56 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: f 101 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7757 (ttt180) REVERT: f 104 LYS cc_start: 0.9148 (mttt) cc_final: 0.8787 (mmmt) REVERT: f 128 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6564 (mmt) REVERT: f 140 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7615 (mp) REVERT: m 53 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: m 168 GLN cc_start: 0.8580 (tp40) cc_final: 0.8190 (tp40) REVERT: m 188 ASP cc_start: 0.8372 (t0) cc_final: 0.8034 (t70) REVERT: m 211 ASN cc_start: 0.9065 (t0) cc_final: 0.8646 (t0) REVERT: n 33 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8433 (ttmm) REVERT: n 50 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6464 (p90) REVERT: n 98 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7932 (mt) REVERT: n 121 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7094 (tt0) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 1.2477 time to fit residues: 211.6902 Evaluate side-chains 164 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU 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 128 MET 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 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 215 VAL Chi-restraints excluded: chain n residue 261 ARG Chi-restraints excluded: chain n residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 92 optimal weight: 0.0970 chunk 5 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN n 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094893 restraints weight = 11443.710| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.89 r_work: 0.2941 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8519 Z= 0.161 Angle : 0.613 12.199 11558 Z= 0.315 Chirality : 0.042 0.185 1299 Planarity : 0.003 0.033 1468 Dihedral : 5.004 58.672 1208 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 3.13 % Allowed : 20.19 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1040 helix: 4.31 (0.30), residues: 237 sheet: 1.38 (0.33), residues: 264 loop : -2.25 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 259 HIS 0.010 0.001 HIS n 48 PHE 0.012 0.001 PHE m 55 TYR 0.028 0.001 TYR m 93 ARG 0.005 0.000 ARG n 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6759.37 seconds wall clock time: 119 minutes 10.57 seconds (7150.57 seconds total)