Starting phenix.real_space_refine on Thu Feb 13 00:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fje_31619/02_2025/7fje_31619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fje_31619/02_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_31619/02_2025/7fje_31619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fje_31619/02_2025/7fje_31619.map" model { file = "/net/cci-nas-00/data/ceres_data/7fje_31619/02_2025/7fje_31619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fje_31619/02_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-5592/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: 5.28, per 1000 atoms: 0.63 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.17 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: 2.30 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2553 1.34 - 1.47: 2224 1.47 - 1.60: 3666 1.60 - 1.73: 0 1.73 - 1.86: 76 Bond restraints: 8519 Sorted by residual: bond pdb=" CA TYR d 79 " pdb=" C TYR d 79 " ideal model delta sigma weight residual 1.523 1.586 -0.063 1.34e-02 5.57e+03 2.20e+01 bond pdb=" C SER e 103 " pdb=" N LYS e 104 " ideal model delta sigma weight residual 1.327 1.233 0.094 2.86e-02 1.22e+03 1.09e+01 bond pdb=" CA SER m 235 " pdb=" CB SER m 235 " ideal model delta sigma weight residual 1.531 1.434 0.097 3.12e-02 1.03e+03 9.61e+00 bond pdb=" CG LEU f 114 " pdb=" CD2 LEU f 114 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB ARG n 228 " pdb=" CG ARG n 228 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 ... (remaining 8514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 11309 3.26 - 6.53: 211 6.53 - 9.79: 29 9.79 - 13.05: 6 13.05 - 16.31: 3 Bond angle restraints: 11558 Sorted by residual: angle pdb=" N ILE d 78 " pdb=" CA ILE d 78 " pdb=" C ILE d 78 " ideal model delta sigma weight residual 109.34 125.08 -15.74 2.08e+00 2.31e-01 5.73e+01 angle pdb=" C PHE m 160 " pdb=" N ASP m 161 " pdb=" CA ASP m 161 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" CA TYR d 79 " pdb=" C TYR d 79 " pdb=" O TYR d 79 " ideal model delta sigma weight residual 120.51 113.15 7.36 1.43e+00 4.89e-01 2.65e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 134.21 -12.41 2.44e+00 1.68e-01 2.59e+01 angle pdb=" C GLU g 67 " pdb=" N ASP g 68 " pdb=" CA ASP g 68 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 11553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 4828 16.48 - 32.97: 228 32.97 - 49.45: 89 49.45 - 65.93: 9 65.93 - 82.42: 8 Dihedral angle restraints: 5162 sinusoidal: 2086 harmonic: 3076 Sorted by residual: dihedral pdb=" CA GLU n 49 " pdb=" C GLU n 49 " pdb=" N TYR n 50 " pdb=" CA TYR n 50 " ideal model delta harmonic sigma weight residual 180.00 127.66 52.34 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ASP d 77 " pdb=" C ASP d 77 " pdb=" N ILE d 78 " pdb=" CA ILE d 78 " ideal model delta harmonic sigma weight residual -180.00 -131.28 -48.72 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -168.42 82.42 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1071 0.086 - 0.173: 212 0.173 - 0.259: 13 0.259 - 0.346: 2 0.346 - 0.432: 1 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CB ILE m 134 " pdb=" CA ILE m 134 " pdb=" CG1 ILE m 134 " pdb=" CG2 ILE m 134 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CG LEU a 27 " pdb=" CB LEU a 27 " pdb=" CD1 LEU a 27 " pdb=" CD2 LEU a 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1296 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR e 111 " -0.019 2.00e-02 2.50e+03 2.10e-02 8.85e+00 pdb=" CG TYR e 111 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR e 111 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR e 111 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR e 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR e 111 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR e 111 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR e 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 90 " -0.021 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR d 90 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR d 90 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR d 90 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR d 90 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR d 90 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR d 90 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR d 90 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN n 194 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.75e+00 pdb=" N PRO n 195 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO n 195 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO n 195 " 0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2178 2.81 - 3.33: 6444 3.33 - 3.85: 12226 3.85 - 4.38: 13205 4.38 - 4.90: 24282 Nonbonded interactions: 58335 Sorted by model distance: nonbonded pdb=" OG SER m 118 " pdb=" OE1 GLN n 116 " model vdw 2.287 3.040 nonbonded pdb=" N ASP m 159 " pdb=" OD1 ASP m 159 " model vdw 2.391 3.120 nonbonded pdb=" OG SER a 23 " pdb=" OE1 GLN d 94 " model vdw 2.405 3.040 nonbonded pdb=" O TYR m 71 " pdb=" NZ LYS m 78 " model vdw 2.441 3.120 nonbonded pdb=" O PHE a 24 " pdb=" OG1 THR m 238 " model vdw 2.451 3.040 ... (remaining 58330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 26 through 54) selection = (chain 'b' and resid 26 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 155)) selection = (chain 'f' and resid 33 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.980 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- 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 : 0.934 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: 1.0975 time to fit residues: 265.8031 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 : 0.929 ------------------------------------------------------------------------------- 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): 0.3068 rms_B_bonded: 2.92 r_work: 0.2914 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.920 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8148 (tppp) cc_final: 0.7351 (tmmm) REVERT: d 29 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7884 (mp) REVERT: e 37 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7968 (mttm) REVERT: e 85 LYS cc_start: 0.8761 (mttt) cc_final: 0.8551 (mmmm) REVERT: e 103 SER cc_start: 0.8975 (t) cc_final: 0.8728 (m) REVERT: e 104 LYS cc_start: 0.8951 (mtpm) cc_final: 0.8685 (mttp) REVERT: e 125 MET cc_start: 0.8646 (tpp) cc_final: 0.8405 (mmm) REVERT: e 128 MET cc_start: 0.7253 (mmm) cc_final: 0.6905 (mmt) REVERT: f 56 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: f 104 LYS cc_start: 0.9214 (mttt) cc_final: 0.8813 (mmmt) REVERT: g 105 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7218 (tp-100) REVERT: m 53 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: m 71 TYR cc_start: 0.6957 (t80) cc_final: 0.5227 (t80) REVERT: m 188 ASP cc_start: 0.8248 (t0) cc_final: 0.7895 (t70) REVERT: n 33 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8077 (tttt) REVERT: n 121 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6762 (mp0) REVERT: n 123 TYR cc_start: 0.7469 (m-80) cc_final: 0.7205 (m-80) REVERT: n 135 ASP cc_start: 0.8584 (t70) cc_final: 0.8356 (t0) outliers start: 33 outliers final: 16 residues processed: 190 average time/residue: 1.0566 time to fit residues: 214.6189 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 : 0.922 ------------------------------------------------------------------------------- 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: 0.4980 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 61 HIS f 51 GLN f 74 ASN g 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094831 restraints weight = 11354.986| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.89 r_work: 0.2931 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8519 Z= 0.161 Angle : 0.607 9.633 11558 Z= 0.319 Chirality : 0.043 0.207 1299 Planarity : 0.004 0.043 1468 Dihedral : 5.792 63.708 1208 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.06 % Favored : 93.75 % Rotamer: Outliers : 4.43 % Allowed : 15.01 % 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: -0.71 (0.25), residues: 1040 helix: 2.94 (0.32), residues: 240 sheet: 0.48 (0.33), residues: 265 loop : -2.81 (0.21), residues: 535 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 0.019 0.001 TYR g 34 ARG 0.003 0.000 ARG f 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8241 (tppp) cc_final: 0.7398 (tmmm) REVERT: d 29 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7792 (mp) REVERT: e 85 LYS cc_start: 0.8859 (mttt) cc_final: 0.8580 (mmmm) REVERT: e 103 SER cc_start: 0.8953 (t) cc_final: 0.8747 (m) REVERT: e 104 LYS cc_start: 0.8913 (mtpm) cc_final: 0.8682 (mtpp) REVERT: e 120 GLU cc_start: 0.8028 (tp30) cc_final: 0.7763 (tp30) REVERT: e 121 ASN cc_start: 0.7929 (m110) cc_final: 0.7254 (m-40) REVERT: e 125 MET cc_start: 0.8784 (tpp) cc_final: 0.8570 (mmm) REVERT: e 128 MET cc_start: 0.7118 (mmm) cc_final: 0.6809 (mmt) REVERT: f 56 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: f 104 LYS cc_start: 0.9229 (mttt) cc_final: 0.8834 (mmmt) REVERT: f 128 MET cc_start: 0.7185 (ttt) cc_final: 0.6714 (mmt) REVERT: f 135 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7875 (mp) REVERT: f 140 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7765 (mp) REVERT: m 47 TYR cc_start: 0.8552 (p90) cc_final: 0.8209 (p90) REVERT: m 53 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: m 71 TYR cc_start: 0.6815 (t80) cc_final: 0.5636 (t80) REVERT: m 188 ASP cc_start: 0.8402 (t0) cc_final: 0.8041 (t70) REVERT: m 211 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8724 (t0) REVERT: n 33 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8395 (ttmm) REVERT: n 121 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6914 (mp0) REVERT: n 123 TYR cc_start: 0.7777 (m-80) cc_final: 0.7437 (m-80) outliers start: 41 outliers final: 18 residues processed: 175 average time/residue: 1.0890 time to fit residues: 203.8596 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 10 optimal weight: 4.9990 chunk 97 optimal weight: 0.0770 chunk 93 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 163 GLN m 168 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 230 GLN n 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091279 restraints weight = 11265.466| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.91 r_work: 0.2877 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3130 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= 0.203 Angle : 0.623 10.170 11558 Z= 0.327 Chirality : 0.043 0.203 1299 Planarity : 0.004 0.042 1468 Dihedral : 5.623 59.001 1208 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 4.54 % Allowed : 16.63 % Favored : 78.83 % 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: -0.45 (0.26), residues: 1040 helix: 3.43 (0.31), residues: 237 sheet: 0.71 (0.34), residues: 248 loop : -2.70 (0.21), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP m 197 HIS 0.003 0.001 HIS e 61 PHE 0.016 0.002 PHE m 55 TYR 0.024 0.002 TYR m 93 ARG 0.004 0.000 ARG f 115 *********************** 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 179 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8219 (tppp) cc_final: 0.7348 (tmmm) REVERT: d 29 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7781 (mp) REVERT: d 92 MET cc_start: 0.8626 (mmm) cc_final: 0.7997 (mmm) REVERT: e 85 LYS cc_start: 0.8879 (mttt) cc_final: 0.8571 (mmmm) REVERT: e 103 SER cc_start: 0.8954 (t) cc_final: 0.8701 (m) REVERT: e 104 LYS cc_start: 0.8960 (mtpm) cc_final: 0.8703 (mtmp) REVERT: e 121 ASN cc_start: 0.7843 (m110) cc_final: 0.7264 (m-40) REVERT: e 128 MET cc_start: 0.7184 (mmm) cc_final: 0.6863 (mmt) REVERT: f 56 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: f 104 LYS cc_start: 0.9206 (mttt) cc_final: 0.8815 (mmmt) REVERT: f 128 MET cc_start: 0.7160 (ttt) cc_final: 0.6665 (mmt) REVERT: f 135 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7895 (mp) REVERT: f 140 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7778 (mp) REVERT: g 65 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8000 (mp) REVERT: m 53 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: m 94 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8315 (pt) REVERT: m 188 ASP cc_start: 0.8266 (t0) cc_final: 0.7928 (t70) REVERT: m 211 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8664 (t0) REVERT: n 33 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8468 (ttmm) REVERT: n 121 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6974 (tt0) REVERT: n 123 TYR cc_start: 0.7859 (m-80) cc_final: 0.7587 (m-80) outliers start: 42 outliers final: 22 residues processed: 162 average time/residue: 1.0904 time to fit residues: 189.1445 Evaluate side-chains 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 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 93 TYR 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 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: 2.9990 chunk 90 optimal weight: 0.0020 chunk 61 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 163 GLN ** m 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.093057 restraints weight = 11171.666| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.84 r_work: 0.2917 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3312 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= 0.168 Angle : 0.592 10.398 11558 Z= 0.311 Chirality : 0.042 0.189 1299 Planarity : 0.004 0.038 1468 Dihedral : 5.427 59.620 1208 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 4.86 % Allowed : 16.74 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (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: -0.23 (0.26), residues: 1040 helix: 3.67 (0.31), residues: 237 sheet: 0.76 (0.34), residues: 254 loop : -2.57 (0.21), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 259 HIS 0.003 0.001 HIS n 226 PHE 0.014 0.001 PHE m 55 TYR 0.028 0.001 TYR m 93 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 182 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8077 (tppp) cc_final: 0.7315 (tmmm) REVERT: d 29 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7784 (mp) REVERT: d 92 MET cc_start: 0.8671 (mmm) cc_final: 0.8095 (mmm) REVERT: e 85 LYS cc_start: 0.8904 (mttt) cc_final: 0.8678 (mtmt) REVERT: e 103 SER cc_start: 0.8891 (t) cc_final: 0.8626 (m) REVERT: e 104 LYS cc_start: 0.8949 (mtpm) cc_final: 0.8737 (mtmp) REVERT: e 128 MET cc_start: 0.7171 (mmm) cc_final: 0.6858 (mmt) REVERT: f 56 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: f 104 LYS cc_start: 0.9202 (mttt) cc_final: 0.8804 (mmmt) REVERT: f 128 MET cc_start: 0.7234 (ttt) cc_final: 0.6717 (mmt) REVERT: f 135 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7875 (mp) REVERT: f 140 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7680 (mp) REVERT: g 51 LYS cc_start: 0.7230 (tppt) cc_final: 0.6970 (tppt) REVERT: g 65 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7897 (mp) REVERT: m 53 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: m 94 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8457 (pt) REVERT: m 188 ASP cc_start: 0.8377 (t0) cc_final: 0.8031 (t70) REVERT: m 211 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8744 (t0) REVERT: n 25 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: n 33 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8433 (ttmm) REVERT: n 121 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7019 (tt0) REVERT: n 123 TYR cc_start: 0.7955 (m-80) cc_final: 0.7664 (m-80) outliers start: 45 outliers final: 26 residues processed: 165 average time/residue: 1.0787 time to fit residues: 190.3721 Evaluate side-chains 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 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 91 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 94 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain m residue 211 ASN Chi-restraints excluded: chain n residue 25 GLN 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: 0.7980 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 163 GLN m 211 ASN n 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090962 restraints weight = 11259.447| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.85 r_work: 0.2883 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8519 Z= 0.213 Angle : 0.625 10.709 11558 Z= 0.327 Chirality : 0.043 0.197 1299 Planarity : 0.004 0.039 1468 Dihedral : 5.426 58.241 1208 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.06 % Favored : 93.85 % Rotamer: Outliers : 5.62 % Allowed : 16.09 % Favored : 78.29 % 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: -0.14 (0.26), residues: 1040 helix: 3.74 (0.31), residues: 237 sheet: 0.95 (0.34), residues: 248 loop : -2.55 (0.21), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP m 197 HIS 0.003 0.001 HIS e 61 PHE 0.013 0.001 PHE e 110 TYR 0.025 0.001 TYR m 93 ARG 0.003 0.000 ARG f 115 *********************** 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 188 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.8096 (tppp) cc_final: 0.7312 (tmmm) REVERT: d 29 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7875 (mp) REVERT: d 92 MET cc_start: 0.8757 (mmm) cc_final: 0.8132 (mmm) REVERT: e 85 LYS cc_start: 0.8899 (mttt) cc_final: 0.8678 (mtmt) REVERT: e 103 SER cc_start: 0.8903 (t) cc_final: 0.8604 (m) REVERT: e 104 LYS cc_start: 0.8972 (mtpm) cc_final: 0.8757 (mtmp) REVERT: e 128 MET cc_start: 0.7291 (mmm) cc_final: 0.6970 (mmt) REVERT: f 56 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: f 104 LYS cc_start: 0.9239 (mttt) cc_final: 0.8812 (mmmt) REVERT: f 128 MET cc_start: 0.7269 (ttt) cc_final: 0.6732 (mmt) REVERT: f 135 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7901 (mp) REVERT: f 140 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7707 (mp) REVERT: g 65 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7891 (mp) REVERT: m 53 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: m 94 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (pt) REVERT: m 143 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8180 (tp40) REVERT: m 188 ASP cc_start: 0.8393 (t0) cc_final: 0.8058 (t70) REVERT: m 211 ASN cc_start: 0.9043 (t0) cc_final: 0.8714 (t0) REVERT: n 25 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8732 (pt0) REVERT: n 33 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8437 (ttmm) REVERT: n 50 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6511 (p90) REVERT: n 121 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7004 (tt0) REVERT: n 123 TYR cc_start: 0.8036 (m-80) cc_final: 0.7785 (m-80) outliers start: 52 outliers final: 24 residues processed: 170 average time/residue: 1.0955 time to fit residues: 199.3818 Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain d residue 123 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 135 ILE Chi-restraints excluded: chain f residue 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 143 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU 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 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 294 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.134596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092184 restraints weight = 11283.628| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.85 r_work: 0.2907 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8519 Z= 0.177 Angle : 0.604 10.644 11558 Z= 0.315 Chirality : 0.042 0.187 1299 Planarity : 0.004 0.036 1468 Dihedral : 5.284 58.271 1208 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 4.75 % Allowed : 17.17 % Favored : 78.08 % 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: 0.02 (0.26), residues: 1040 helix: 3.89 (0.30), residues: 237 sheet: 0.99 (0.34), residues: 252 loop : -2.46 (0.22), residues: 551 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 0.013 0.001 PHE m 55 TYR 0.020 0.001 TYR g 34 ARG 0.002 0.000 ARG f 115 *********************** 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 184 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.850 Fit side-chains REVERT: b 54 LYS cc_start: 0.8089 (tppp) cc_final: 0.7287 (tmmm) REVERT: d 29 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7773 (mp) REVERT: d 92 MET cc_start: 0.8742 (mmm) cc_final: 0.8121 (mmm) REVERT: e 85 LYS cc_start: 0.8888 (mttt) cc_final: 0.8672 (mtmt) REVERT: e 103 SER cc_start: 0.8874 (t) cc_final: 0.8587 (m) REVERT: e 104 LYS cc_start: 0.8983 (mtpm) cc_final: 0.8745 (mtmp) REVERT: e 128 MET cc_start: 0.7192 (mmm) cc_final: 0.6883 (mmt) REVERT: f 56 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: f 104 LYS cc_start: 0.9235 (mttt) cc_final: 0.8817 (mmmt) REVERT: f 128 MET cc_start: 0.7169 (ttt) cc_final: 0.6643 (mmt) REVERT: f 140 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7691 (mp) REVERT: m 53 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: m 188 ASP cc_start: 0.8385 (t0) cc_final: 0.8056 (t70) REVERT: m 211 ASN cc_start: 0.9068 (t0) cc_final: 0.8681 (t0) REVERT: n 33 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8407 (ttmm) REVERT: n 50 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6307 (p90) REVERT: n 121 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7001 (tt0) REVERT: n 123 TYR cc_start: 0.8114 (m-80) cc_final: 0.7897 (m-80) outliers start: 44 outliers final: 27 residues processed: 167 average time/residue: 1.0844 time to fit residues: 193.8397 Evaluate side-chains 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 136 VAL Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain 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 294 VAL Chi-restraints excluded: chain n residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 0.0870 chunk 53 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.138106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096149 restraints weight = 11409.994| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.88 r_work: 0.2957 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8519 Z= 0.138 Angle : 0.570 10.489 11558 Z= 0.296 Chirality : 0.041 0.183 1299 Planarity : 0.003 0.033 1468 Dihedral : 5.013 59.094 1208 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 3.13 % Allowed : 18.79 % Favored : 78.08 % 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: 0.32 (0.26), residues: 1040 helix: 4.13 (0.30), residues: 237 sheet: 1.16 (0.33), residues: 272 loop : -2.37 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 259 HIS 0.002 0.000 HIS n 226 PHE 0.013 0.001 PHE m 55 TYR 0.016 0.001 TYR g 34 ARG 0.003 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 183 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.762 Fit side-chains REVERT: b 54 LYS cc_start: 0.8024 (tppp) cc_final: 0.7239 (tmmm) REVERT: d 92 MET cc_start: 0.8654 (mmm) cc_final: 0.8027 (mmm) REVERT: e 85 LYS cc_start: 0.8890 (mttt) cc_final: 0.8669 (mtmt) REVERT: e 103 SER cc_start: 0.8845 (t) cc_final: 0.8564 (m) REVERT: e 128 MET cc_start: 0.6927 (mmm) cc_final: 0.6633 (mmt) REVERT: f 56 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: f 101 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7790 (ttt180) REVERT: f 104 LYS cc_start: 0.9193 (mttt) cc_final: 0.8830 (mmmt) REVERT: f 128 MET cc_start: 0.7082 (ttt) cc_final: 0.6554 (mmt) REVERT: f 140 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7638 (mp) REVERT: g 131 VAL cc_start: 0.8386 (t) cc_final: 0.8157 (t) REVERT: g 135 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6692 (t80) REVERT: m 53 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: m 71 TYR cc_start: 0.7030 (t80) cc_final: 0.6045 (t80) REVERT: m 182 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (tt) REVERT: m 188 ASP cc_start: 0.8357 (t0) cc_final: 0.8024 (t70) REVERT: m 211 ASN cc_start: 0.9084 (t0) cc_final: 0.8704 (t0) REVERT: n 33 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8420 (ttmm) REVERT: n 50 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6337 (p90) REVERT: n 98 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7900 (mt) REVERT: n 121 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6985 (mp0) REVERT: n 123 TYR cc_start: 0.8043 (m-80) cc_final: 0.7729 (m-80) REVERT: n 250 VAL cc_start: 0.8730 (m) cc_final: 0.8418 (t) outliers start: 29 outliers final: 16 residues processed: 171 average time/residue: 1.0934 time to fit residues: 200.0005 Evaluate side-chains 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 124 GLU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 76 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.137000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094711 restraints weight = 11408.944| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.89 r_work: 0.2937 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8519 Z= 0.157 Angle : 0.605 10.709 11558 Z= 0.310 Chirality : 0.041 0.178 1299 Planarity : 0.003 0.032 1468 Dihedral : 5.015 58.829 1208 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 3.13 % Allowed : 19.01 % Favored : 77.86 % 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: 0.38 (0.26), residues: 1040 helix: 4.21 (0.30), residues: 237 sheet: 1.16 (0.33), residues: 264 loop : -2.27 (0.23), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 259 HIS 0.002 0.001 HIS n 226 PHE 0.012 0.001 PHE m 55 TYR 0.017 0.001 TYR b 42 ARG 0.002 0.000 ARG m 99 *********************** 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 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.899 Fit side-chains REVERT: b 54 LYS cc_start: 0.8003 (tppp) cc_final: 0.7223 (tmmm) REVERT: d 92 MET cc_start: 0.8691 (mmm) cc_final: 0.8135 (mmm) REVERT: e 103 SER cc_start: 0.8798 (t) cc_final: 0.8500 (m) REVERT: e 128 MET cc_start: 0.7007 (mmm) cc_final: 0.6743 (mmt) REVERT: f 56 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: f 104 LYS cc_start: 0.9164 (mttt) cc_final: 0.8806 (mmmt) REVERT: f 128 MET cc_start: 0.7081 (ttt) cc_final: 0.6543 (mmt) REVERT: f 140 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7717 (mp) REVERT: g 131 VAL cc_start: 0.8451 (t) cc_final: 0.8222 (t) REVERT: m 53 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: m 182 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8241 (tt) REVERT: m 188 ASP cc_start: 0.8388 (t0) cc_final: 0.8025 (t70) REVERT: m 211 ASN cc_start: 0.9078 (t0) cc_final: 0.8668 (t0) REVERT: n 33 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8502 (ttmm) REVERT: n 50 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6495 (p90) REVERT: n 98 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7910 (mt) REVERT: n 121 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7018 (tt0) REVERT: n 123 TYR cc_start: 0.8041 (m-80) cc_final: 0.7824 (m-80) outliers start: 29 outliers final: 14 residues processed: 162 average time/residue: 1.0697 time to fit residues: 185.6218 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 102 GLN m 163 GLN n 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094386 restraints weight = 11396.680| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.89 r_work: 0.2932 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8519 Z= 0.163 Angle : 0.602 10.768 11558 Z= 0.313 Chirality : 0.042 0.177 1299 Planarity : 0.003 0.032 1468 Dihedral : 5.002 59.055 1208 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 2.70 % Allowed : 19.55 % Favored : 77.75 % 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: 0.49 (0.26), residues: 1040 helix: 4.26 (0.30), residues: 237 sheet: 1.31 (0.33), residues: 270 loop : -2.29 (0.23), residues: 533 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 0.018 0.001 TYR g 34 ARG 0.003 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 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.818 Fit side-chains REVERT: b 54 LYS cc_start: 0.8001 (tppp) cc_final: 0.7224 (tmmm) REVERT: d 29 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7829 (mt) REVERT: d 92 MET cc_start: 0.8709 (mmm) cc_final: 0.8161 (mmm) REVERT: e 103 SER cc_start: 0.8811 (t) cc_final: 0.8539 (m) REVERT: e 104 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8587 (mtpp) REVERT: e 128 MET cc_start: 0.7026 (mmm) cc_final: 0.6750 (mmt) REVERT: f 56 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8069 (mm-30) REVERT: f 104 LYS cc_start: 0.9161 (mttt) cc_final: 0.8805 (mmmt) REVERT: f 128 MET cc_start: 0.7094 (ttt) cc_final: 0.6556 (mmt) REVERT: f 140 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7675 (mp) REVERT: g 131 VAL cc_start: 0.8482 (t) cc_final: 0.8247 (t) REVERT: m 53 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: m 113 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7834 (ptt) REVERT: m 188 ASP cc_start: 0.8390 (t0) cc_final: 0.8030 (t70) REVERT: m 211 ASN cc_start: 0.9085 (t0) cc_final: 0.8694 (t0) REVERT: n 33 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8465 (ttmm) REVERT: n 50 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6503 (p90) REVERT: n 98 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7914 (mt) REVERT: n 121 GLU cc_start: 0.7672 (mt-10) cc_final: 0.6995 (tt0) REVERT: n 123 TYR cc_start: 0.8095 (m-80) cc_final: 0.7888 (m-80) outliers start: 25 outliers final: 16 residues processed: 159 average time/residue: 1.0670 time to fit residues: 181.5811 Evaluate side-chains 165 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain m residue 53 GLN Chi-restraints excluded: chain m residue 113 MET Chi-restraints excluded: chain m residue 154 VAL Chi-restraints excluded: chain m residue 182 LEU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 50 TYR Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 137 LYS Chi-restraints excluded: chain n residue 199 GLN Chi-restraints excluded: chain n residue 204 ASP Chi-restraints excluded: chain n residue 261 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 121 ASN m 102 GLN m 163 GLN n 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095065 restraints weight = 11465.719| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.89 r_work: 0.2933 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8519 Z= 0.156 Angle : 0.600 10.634 11558 Z= 0.311 Chirality : 0.041 0.173 1299 Planarity : 0.003 0.032 1468 Dihedral : 4.960 60.131 1208 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.81 % Allowed : 19.55 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (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: 0.57 (0.27), residues: 1040 helix: 4.32 (0.30), residues: 237 sheet: 1.35 (0.33), residues: 270 loop : -2.23 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 259 HIS 0.008 0.001 HIS n 48 PHE 0.011 0.001 PHE m 55 TYR 0.018 0.001 TYR b 42 ARG 0.002 0.000 ARG m 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6709.50 seconds wall clock time: 118 minutes 39.51 seconds (7119.51 seconds total)