Starting phenix.real_space_refine on Wed Mar 4 19:26:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ucl_64047/03_2026/9ucl_64047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ucl_64047/03_2026/9ucl_64047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ucl_64047/03_2026/9ucl_64047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ucl_64047/03_2026/9ucl_64047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ucl_64047/03_2026/9ucl_64047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ucl_64047/03_2026/9ucl_64047.map" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 48 5.16 5 C 9897 2.51 5 N 2661 2.21 5 O 2943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15549 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2424 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 305} Chain: "B" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2424 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 305} Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2424 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 305} Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1872 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "E" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1872 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "F" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1872 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain: "G" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 107} Chain: "H" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 107} Chain: "I" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 107} Time building chain proxies: 3.46, per 1000 atoms: 0.22 Number of scatterers: 15549 At special positions: 0 Unit cell: (121.44, 131.56, 122.36, 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 48 16.00 O 2943 8.00 N 2661 7.00 C 9897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 99 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.07 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " 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: 1.28 Conformation dependent library (CDL) restraints added in 547.8 milliseconds 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 26 sheets defined 50.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 28 through 42 Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.551A pdb=" N ILE A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 126 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.539A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.889A pdb=" N VAL A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 4.069A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 301 through 320 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 27 through 42 removed outlier: 3.523A pdb=" N VAL B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 59 through 71 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 93 through 126 Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.808A pdb=" N VAL B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 removed outlier: 4.103A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 301 through 320 Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 27 through 42 Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 93 through 126 Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.640A pdb=" N ALA C 146 " --> pdb=" O GLU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 188 through 199 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.819A pdb=" N VAL C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.069A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 286 Processing helix chain 'C' and resid 301 through 320 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 128 through 142 removed outlier: 4.219A pdb=" N HIS D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.576A pdb=" N LYS D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 192 through 207 Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.625A pdb=" N TRP D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 244 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 128 through 142 removed outlier: 4.304A pdb=" N HIS E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 156 Processing helix chain 'E' and resid 158 through 172 Processing helix chain 'E' and resid 176 through 191 Processing helix chain 'E' and resid 192 through 207 Processing helix chain 'E' and resid 207 through 222 removed outlier: 3.799A pdb=" N GLY E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 128 through 143 removed outlier: 4.227A pdb=" N HIS F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 156 removed outlier: 3.636A pdb=" N LYS F 156 " --> pdb=" O ALA F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 192 through 207 Processing helix chain 'F' and resid 207 through 222 removed outlier: 3.720A pdb=" N GLY F 222 " --> pdb=" O ALA F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 244 Processing helix chain 'I' and resid 61 through 65 removed outlier: 4.208A pdb=" N GLU I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 184 removed outlier: 6.542A pdb=" N ILE A 155 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY A 184 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 157 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 154 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.660A pdb=" N ILE A 203 " --> pdb=" O MET A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 184 removed outlier: 6.470A pdb=" N ILE B 155 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY B 184 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE B 157 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU B 154 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'C' and resid 180 through 184 removed outlier: 6.721A pdb=" N ILE C 128 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU C 156 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA C 130 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C 158 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU C 132 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 202 through 204 Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AB1, first strand: chain 'D' and resid 7 through 9 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 14 removed outlier: 5.968A pdb=" N ARG D 40 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB4, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.883A pdb=" N MET E 36 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA E 52 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP E 38 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AB6, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.347A pdb=" N GLY F 12 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N MET F 36 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ALA F 52 " --> pdb=" O MET F 36 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP F 38 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.347A pdb=" N GLY F 12 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.204A pdb=" N VAL G 10 " --> pdb=" O ARG G 114 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY G 93 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 94 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY G 33 " --> pdb=" O HIS G 53 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS G 53 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL G 35 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AC3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.510A pdb=" N VAL H 12 " --> pdb=" O ARG H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.768A pdb=" N TRP H 37 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU H 51 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL H 35 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 68 through 69 Processing sheet with id=AC7, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.505A pdb=" N CYS I 97 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL I 35 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 68 through 69 923 hydrogen bonds defined for protein. 2628 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: 2.72 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3028 1.33 - 1.45: 3581 1.45 - 1.57: 9150 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 15831 Sorted by residual: bond pdb=" CA SER D 78 " pdb=" CB SER D 78 " ideal model delta sigma weight residual 1.532 1.463 0.069 1.62e-02 3.81e+03 1.82e+01 bond pdb=" C PRO I 71 " pdb=" N PRO I 72 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.76e+01 bond pdb=" CA SER E 27 " pdb=" CB SER E 27 " ideal model delta sigma weight residual 1.528 1.462 0.066 1.61e-02 3.86e+03 1.66e+01 bond pdb=" CA SER F 27 " pdb=" CB SER F 27 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.35e-02 5.49e+03 1.49e+01 bond pdb=" CA SER D 27 " pdb=" CB SER D 27 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.70e-02 3.46e+03 1.47e+01 ... (remaining 15826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 20698 2.43 - 4.86: 546 4.86 - 7.28: 121 7.28 - 9.71: 27 9.71 - 12.14: 7 Bond angle restraints: 21399 Sorted by residual: angle pdb=" CA PHE E 30 " pdb=" CB PHE E 30 " pdb=" CG PHE E 30 " ideal model delta sigma weight residual 113.80 124.17 -10.37 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE D 71 " pdb=" CB PHE D 71 " pdb=" CG PHE D 71 " ideal model delta sigma weight residual 113.80 122.40 -8.60 1.00e+00 1.00e+00 7.40e+01 angle pdb=" CA PHE F 30 " pdb=" CB PHE F 30 " pdb=" CG PHE F 30 " ideal model delta sigma weight residual 113.80 121.66 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" N PHE D 33 " pdb=" CA PHE D 33 " pdb=" C PHE D 33 " ideal model delta sigma weight residual 114.09 101.95 12.14 1.55e+00 4.16e-01 6.14e+01 angle pdb=" N SER E 31 " pdb=" CA SER E 31 " pdb=" C SER E 31 " ideal model delta sigma weight residual 112.25 122.80 -10.55 1.36e+00 5.41e-01 6.02e+01 ... (remaining 21394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 8198 18.17 - 36.33: 987 36.33 - 54.50: 344 54.50 - 72.67: 62 72.67 - 90.83: 36 Dihedral angle restraints: 9627 sinusoidal: 3822 harmonic: 5805 Sorted by residual: dihedral pdb=" C ARG D 29 " pdb=" N ARG D 29 " pdb=" CA ARG D 29 " pdb=" CB ARG D 29 " ideal model delta harmonic sigma weight residual -122.60 -110.32 -12.28 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C SER F 31 " pdb=" N SER F 31 " pdb=" CA SER F 31 " pdb=" CB SER F 31 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" C SER E 31 " pdb=" N SER E 31 " pdb=" CA SER E 31 " pdb=" CB SER E 31 " ideal model delta harmonic sigma weight residual -122.60 -134.07 11.47 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 9624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2337 0.135 - 0.270: 62 0.270 - 0.404: 9 0.404 - 0.539: 1 0.539 - 0.674: 3 Chirality restraints: 2412 Sorted by residual: chirality pdb=" CG LEU H 51 " pdb=" CB LEU H 51 " pdb=" CD1 LEU H 51 " pdb=" CD2 LEU H 51 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CG LEU G 51 " pdb=" CB LEU G 51 " pdb=" CD1 LEU G 51 " pdb=" CD2 LEU G 51 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA SER E 31 " pdb=" N SER E 31 " pdb=" C SER E 31 " pdb=" CB SER E 31 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.94e+00 ... (remaining 2409 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 25 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ALA E 25 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA E 25 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA E 26 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 59 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C HIS H 59 " -0.062 2.00e-02 2.50e+03 pdb=" O HIS H 59 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL H 60 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 25 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ALA D 25 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA D 25 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA D 26 " -0.019 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1165 2.74 - 3.28: 15533 3.28 - 3.82: 26551 3.82 - 4.36: 31301 4.36 - 4.90: 53569 Nonbonded interactions: 128119 Sorted by model distance: nonbonded pdb=" O LEU B 277 " pdb=" NZ LYS B 315 " model vdw 2.198 3.120 nonbonded pdb=" O LEU A 277 " pdb=" NZ LYS A 315 " model vdw 2.207 3.120 nonbonded pdb=" OD2 ASP E 109 " pdb=" OG SER E 111 " model vdw 2.230 3.040 nonbonded pdb=" O LYS C 194 " pdb=" OG SER C 198 " model vdw 2.230 3.040 nonbonded pdb=" OG SER A 205 " pdb=" O HIS A 207 " model vdw 2.241 3.040 ... (remaining 128114 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 : 0.004 0.069 15840 Z= 0.281 Angle : 0.927 12.141 21417 Z= 0.596 Chirality : 0.060 0.674 2412 Planarity : 0.005 0.081 2775 Dihedral : 18.579 90.832 5862 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.42 % Allowed : 31.60 % Favored : 65.98 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 2013 helix: 1.51 (0.16), residues: 969 sheet: -0.79 (0.25), residues: 435 loop : -1.17 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.022 0.001 TYR E 34 PHE 0.034 0.001 PHE E 30 TRP 0.028 0.002 TRP G 37 HIS 0.006 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00432 (15831) covalent geometry : angle 0.92471 (21399) SS BOND : bond 0.01395 ( 9) SS BOND : angle 2.52293 ( 18) hydrogen bonds : bond 0.19752 ( 912) hydrogen bonds : angle 6.71086 ( 2628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 492 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6576 (tm-30) REVERT: A 213 SER cc_start: 0.7975 (p) cc_final: 0.7769 (p) REVERT: B 48 ARG cc_start: 0.7069 (ttt-90) cc_final: 0.6611 (ttp-110) REVERT: B 142 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6780 (mt-10) REVERT: C 26 ASP cc_start: 0.7187 (p0) cc_final: 0.6697 (p0) REVERT: C 77 ASP cc_start: 0.7124 (p0) cc_final: 0.6879 (p0) REVERT: C 138 GLU cc_start: 0.6951 (tt0) cc_final: 0.6437 (tt0) REVERT: C 142 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6584 (mt-10) REVERT: C 217 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7785 (ttpt) REVERT: F 3 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7249 (mt-10) REVERT: F 30 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: F 46 GLU cc_start: 0.7816 (tp30) cc_final: 0.7272 (tp30) REVERT: F 235 LYS cc_start: 0.7213 (tptm) cc_final: 0.6992 (tptm) REVERT: G 40 VAL cc_start: 0.8196 (m) cc_final: 0.7948 (p) outliers start: 39 outliers final: 26 residues processed: 516 average time/residue: 0.8206 time to fit residues: 454.4694 Evaluate side-chains 511 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 484 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 60 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN H 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.164012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.155825 restraints weight = 22527.795| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.56 r_work: 0.4032 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15840 Z= 0.132 Angle : 0.573 8.155 21417 Z= 0.293 Chirality : 0.041 0.229 2412 Planarity : 0.004 0.046 2775 Dihedral : 6.719 78.148 2206 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.72 % Allowed : 29.42 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 2013 helix: 2.35 (0.16), residues: 978 sheet: -0.71 (0.25), residues: 441 loop : -0.82 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 25 TYR 0.014 0.001 TYR D 34 PHE 0.018 0.001 PHE F 30 TRP 0.016 0.001 TRP E 112 HIS 0.007 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00286 (15831) covalent geometry : angle 0.57071 (21399) SS BOND : bond 0.00325 ( 9) SS BOND : angle 1.76009 ( 18) hydrogen bonds : bond 0.03925 ( 912) hydrogen bonds : angle 4.44137 ( 2628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 532 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7519 (m-30) cc_final: 0.7288 (m-30) REVERT: A 23 LYS cc_start: 0.8343 (mttp) cc_final: 0.8123 (mttp) REVERT: A 27 ARG cc_start: 0.7627 (mmt-90) cc_final: 0.6668 (mmt-90) REVERT: A 70 LEU cc_start: 0.8613 (mp) cc_final: 0.8380 (mp) REVERT: B 25 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7703 (ptt-90) REVERT: B 48 ARG cc_start: 0.7555 (ttt-90) cc_final: 0.7063 (ttp-110) REVERT: B 209 ASP cc_start: 0.7130 (t70) cc_final: 0.6657 (t70) REVERT: B 217 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7850 (ttpp) REVERT: C 26 ASP cc_start: 0.7279 (p0) cc_final: 0.6665 (p0) REVERT: C 142 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6717 (mt-10) REVERT: D 212 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7601 (mmtm) REVERT: D 227 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7568 (mtmt) REVERT: D 242 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8109 (ttpt) REVERT: F 46 GLU cc_start: 0.7644 (tp30) cc_final: 0.7170 (tp30) REVERT: F 187 LYS cc_start: 0.8092 (mttm) cc_final: 0.7863 (mtpt) REVERT: G 40 VAL cc_start: 0.8150 (m) cc_final: 0.7891 (p) outliers start: 76 outliers final: 41 residues processed: 557 average time/residue: 0.7649 time to fit residues: 458.3026 Evaluate side-chains 552 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 511 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 101 optimal weight: 0.5980 chunk 127 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 183 optimal weight: 0.0050 chunk 45 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.164895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.156140 restraints weight = 22509.444| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.66 r_work: 0.4025 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15840 Z= 0.123 Angle : 0.535 7.384 21417 Z= 0.270 Chirality : 0.040 0.153 2412 Planarity : 0.004 0.040 2775 Dihedral : 5.608 67.267 2175 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.84 % Allowed : 30.29 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2013 helix: 2.57 (0.16), residues: 981 sheet: -0.36 (0.26), residues: 414 loop : -1.07 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.012 0.001 TYR G 56 PHE 0.013 0.001 PHE F 49 TRP 0.014 0.001 TRP E 112 HIS 0.005 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00274 (15831) covalent geometry : angle 0.53385 (21399) SS BOND : bond 0.00414 ( 9) SS BOND : angle 1.22856 ( 18) hydrogen bonds : bond 0.03416 ( 912) hydrogen bonds : angle 4.05071 ( 2628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 508 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7512 (m-30) cc_final: 0.7275 (m-30) REVERT: A 23 LYS cc_start: 0.8357 (mttp) cc_final: 0.8141 (mttp) REVERT: A 81 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7391 (ttm170) REVERT: B 48 ARG cc_start: 0.7607 (ttt-90) cc_final: 0.7061 (ttp-110) REVERT: C 26 ASP cc_start: 0.7460 (p0) cc_final: 0.6802 (p0) REVERT: C 142 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6766 (mt-10) REVERT: D 212 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7637 (mmtm) REVERT: E 238 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: F 3 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6935 (mt-10) REVERT: F 46 GLU cc_start: 0.7709 (tp30) cc_final: 0.7286 (tp30) REVERT: G 40 VAL cc_start: 0.8138 (m) cc_final: 0.7878 (p) REVERT: H 16 GLN cc_start: 0.5531 (OUTLIER) cc_final: 0.5263 (mt0) outliers start: 78 outliers final: 44 residues processed: 540 average time/residue: 0.8057 time to fit residues: 467.4226 Evaluate side-chains 550 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 504 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 132 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 122 optimal weight: 0.0170 chunk 140 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.164178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155288 restraints weight = 22332.135| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.67 r_work: 0.4013 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15840 Z= 0.148 Angle : 0.540 8.185 21417 Z= 0.272 Chirality : 0.041 0.148 2412 Planarity : 0.004 0.042 2775 Dihedral : 5.227 59.185 2167 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.84 % Allowed : 30.54 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2013 helix: 2.67 (0.16), residues: 981 sheet: -0.23 (0.27), residues: 414 loop : -1.07 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.011 0.001 TYR D 83 PHE 0.013 0.001 PHE F 49 TRP 0.025 0.001 TRP E 112 HIS 0.004 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00334 (15831) covalent geometry : angle 0.53958 (21399) SS BOND : bond 0.00534 ( 9) SS BOND : angle 1.12901 ( 18) hydrogen bonds : bond 0.03309 ( 912) hydrogen bonds : angle 3.93151 ( 2628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 500 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6630 (mt-10) REVERT: A 20 ASP cc_start: 0.7495 (m-30) cc_final: 0.7250 (m-30) REVERT: A 23 LYS cc_start: 0.8361 (mttp) cc_final: 0.8150 (mttp) REVERT: A 81 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7386 (ttm170) REVERT: A 260 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7995 (mmt) REVERT: B 48 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7052 (ttp-110) REVERT: C 26 ASP cc_start: 0.7409 (p0) cc_final: 0.6790 (p0) REVERT: C 142 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6784 (mt-10) REVERT: C 209 ASP cc_start: 0.7003 (t0) cc_final: 0.6236 (t0) REVERT: C 211 GLU cc_start: 0.7339 (mp0) cc_final: 0.7033 (mp0) REVERT: D 34 TYR cc_start: 0.7900 (m-80) cc_final: 0.7555 (m-80) REVERT: D 212 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7712 (mmtm) REVERT: F 3 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7033 (mt-10) REVERT: F 46 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7376 (mm-30) REVERT: G 40 VAL cc_start: 0.8135 (m) cc_final: 0.7865 (p) outliers start: 78 outliers final: 53 residues processed: 526 average time/residue: 0.8232 time to fit residues: 465.2213 Evaluate side-chains 546 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 491 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 138 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 142 HIS F 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.164078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.155080 restraints weight = 22363.869| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.69 r_work: 0.4011 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15840 Z= 0.142 Angle : 0.539 7.680 21417 Z= 0.270 Chirality : 0.040 0.150 2412 Planarity : 0.004 0.041 2775 Dihedral : 5.061 58.072 2167 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.09 % Allowed : 30.11 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 2013 helix: 2.71 (0.16), residues: 981 sheet: -0.16 (0.27), residues: 396 loop : -1.12 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.012 0.001 TYR D 83 PHE 0.014 0.001 PHE F 49 TRP 0.025 0.001 TRP E 112 HIS 0.009 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00321 (15831) covalent geometry : angle 0.53858 (21399) SS BOND : bond 0.00428 ( 9) SS BOND : angle 1.05278 ( 18) hydrogen bonds : bond 0.03199 ( 912) hydrogen bonds : angle 3.86352 ( 2628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 503 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7463 (m-30) cc_final: 0.7246 (m-30) REVERT: A 23 LYS cc_start: 0.8385 (mttp) cc_final: 0.8177 (mttp) REVERT: A 77 ASP cc_start: 0.7426 (m-30) cc_final: 0.7204 (m-30) REVERT: A 81 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7385 (ttm170) REVERT: A 217 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7984 (ttpm) REVERT: A 260 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8014 (mmt) REVERT: C 26 ASP cc_start: 0.7454 (p0) cc_final: 0.6817 (p0) REVERT: C 52 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6996 (mm-30) REVERT: C 81 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7416 (ttm110) REVERT: C 142 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6782 (mt-10) REVERT: C 209 ASP cc_start: 0.7035 (t0) cc_final: 0.6447 (t0) REVERT: D 212 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7679 (mmtm) REVERT: F 46 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: G 40 VAL cc_start: 0.8139 (m) cc_final: 0.7866 (p) REVERT: I 67 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6776 (ttp-170) outliers start: 82 outliers final: 53 residues processed: 534 average time/residue: 0.8100 time to fit residues: 464.1277 Evaluate side-chains 554 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 497 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.0040 chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.155865 restraints weight = 22232.297| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.68 r_work: 0.4021 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15840 Z= 0.112 Angle : 0.531 7.758 21417 Z= 0.265 Chirality : 0.040 0.163 2412 Planarity : 0.003 0.042 2775 Dihedral : 4.800 58.099 2164 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.78 % Allowed : 31.28 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 2013 helix: 2.77 (0.16), residues: 981 sheet: -0.33 (0.25), residues: 444 loop : -1.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.009 0.001 TYR D 240 PHE 0.013 0.001 PHE F 49 TRP 0.022 0.001 TRP E 112 HIS 0.008 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00254 (15831) covalent geometry : angle 0.53054 (21399) SS BOND : bond 0.00340 ( 9) SS BOND : angle 0.90462 ( 18) hydrogen bonds : bond 0.02977 ( 912) hydrogen bonds : angle 3.79649 ( 2628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 503 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7435 (m-30) cc_final: 0.7208 (m-30) REVERT: A 27 ARG cc_start: 0.7702 (mmt-90) cc_final: 0.7429 (mmt-90) REVERT: A 81 ARG cc_start: 0.7764 (ttm170) cc_final: 0.7357 (ttm170) REVERT: A 217 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7945 (ttpm) REVERT: A 260 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8084 (mmt) REVERT: B 209 ASP cc_start: 0.7171 (t70) cc_final: 0.6621 (t70) REVERT: B 217 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7872 (ttpp) REVERT: C 26 ASP cc_start: 0.7436 (p0) cc_final: 0.6822 (p0) REVERT: C 52 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7004 (mm-30) REVERT: C 81 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7390 (ttm110) REVERT: C 142 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6821 (mt-10) REVERT: C 209 ASP cc_start: 0.7020 (t0) cc_final: 0.6416 (t0) REVERT: E 234 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6542 (mt-10) REVERT: E 238 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: F 46 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: G 40 VAL cc_start: 0.8159 (m) cc_final: 0.7884 (p) REVERT: I 67 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6779 (ttp-170) outliers start: 77 outliers final: 51 residues processed: 531 average time/residue: 0.8175 time to fit residues: 466.1726 Evaluate side-chains 558 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 502 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 189 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.164120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.155189 restraints weight = 22221.413| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.67 r_work: 0.4012 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15840 Z= 0.145 Angle : 0.555 10.326 21417 Z= 0.275 Chirality : 0.040 0.165 2412 Planarity : 0.004 0.041 2775 Dihedral : 4.608 56.860 2162 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.53 % Allowed : 32.15 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.19), residues: 2013 helix: 2.76 (0.16), residues: 981 sheet: -0.34 (0.25), residues: 444 loop : -1.09 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.011 0.001 TYR D 34 PHE 0.019 0.001 PHE A 123 TRP 0.029 0.001 TRP E 112 HIS 0.009 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00332 (15831) covalent geometry : angle 0.55480 (21399) SS BOND : bond 0.00536 ( 9) SS BOND : angle 1.10445 ( 18) hydrogen bonds : bond 0.03136 ( 912) hydrogen bonds : angle 3.78211 ( 2628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 513 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6647 (mt-10) REVERT: A 20 ASP cc_start: 0.7449 (m-30) cc_final: 0.7223 (m-30) REVERT: A 27 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7460 (mmt-90) REVERT: A 81 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7430 (ttm170) REVERT: A 217 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7994 (ttpm) REVERT: A 260 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8028 (mmt) REVERT: B 209 ASP cc_start: 0.7202 (t70) cc_final: 0.6701 (t70) REVERT: C 26 ASP cc_start: 0.7391 (p0) cc_final: 0.6774 (p0) REVERT: C 52 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 81 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7416 (ttm110) REVERT: C 142 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 209 ASP cc_start: 0.7107 (t0) cc_final: 0.6861 (t0) REVERT: I 67 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6826 (ttp-170) outliers start: 73 outliers final: 50 residues processed: 538 average time/residue: 0.8144 time to fit residues: 470.9007 Evaluate side-chains 557 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 504 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 147 optimal weight: 0.0270 chunk 119 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 181 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.165302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.156262 restraints weight = 22333.739| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.70 r_work: 0.4022 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15840 Z= 0.116 Angle : 0.547 9.366 21417 Z= 0.270 Chirality : 0.040 0.182 2412 Planarity : 0.003 0.041 2775 Dihedral : 4.522 56.007 2162 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.16 % Allowed : 33.33 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.19), residues: 2013 helix: 2.77 (0.16), residues: 981 sheet: -0.29 (0.25), residues: 444 loop : -1.08 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.010 0.001 TYR F 237 PHE 0.013 0.001 PHE F 49 TRP 0.027 0.001 TRP E 112 HIS 0.008 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00265 (15831) covalent geometry : angle 0.54637 (21399) SS BOND : bond 0.00405 ( 9) SS BOND : angle 1.01152 ( 18) hydrogen bonds : bond 0.02964 ( 912) hydrogen bonds : angle 3.73819 ( 2628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 502 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6621 (mt-10) REVERT: A 20 ASP cc_start: 0.7416 (m-30) cc_final: 0.7190 (m-30) REVERT: A 27 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.7466 (mmt-90) REVERT: A 81 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7508 (ttm170) REVERT: A 217 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7982 (ttpm) REVERT: A 260 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8104 (mmt) REVERT: B 209 ASP cc_start: 0.7224 (t70) cc_final: 0.6751 (t70) REVERT: B 217 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7867 (ttpp) REVERT: C 26 ASP cc_start: 0.7368 (p0) cc_final: 0.6781 (p0) REVERT: C 52 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 81 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7415 (ttm110) REVERT: C 142 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6823 (mt-10) REVERT: C 209 ASP cc_start: 0.7076 (t0) cc_final: 0.6790 (t0) REVERT: E 234 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6525 (mt-10) REVERT: E 238 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: F 46 GLU cc_start: 0.7630 (tp30) cc_final: 0.7256 (tp30) REVERT: F 227 LYS cc_start: 0.6781 (mttt) cc_final: 0.6374 (mptt) REVERT: I 67 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6827 (ttp-170) outliers start: 67 outliers final: 46 residues processed: 523 average time/residue: 0.7992 time to fit residues: 448.8612 Evaluate side-chains 556 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 506 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 127 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.164701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155812 restraints weight = 22366.057| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.65 r_work: 0.4019 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15840 Z= 0.143 Angle : 0.565 9.900 21417 Z= 0.278 Chirality : 0.041 0.232 2412 Planarity : 0.004 0.041 2775 Dihedral : 4.447 53.844 2160 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.91 % Allowed : 33.71 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.19), residues: 2013 helix: 2.76 (0.16), residues: 981 sheet: -0.45 (0.26), residues: 390 loop : -0.87 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.014 0.001 TYR D 34 PHE 0.012 0.001 PHE F 49 TRP 0.025 0.001 TRP E 112 HIS 0.009 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00330 (15831) covalent geometry : angle 0.56438 (21399) SS BOND : bond 0.00405 ( 9) SS BOND : angle 1.16062 ( 18) hydrogen bonds : bond 0.03114 ( 912) hydrogen bonds : angle 3.76139 ( 2628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 503 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6577 (mt-10) REVERT: A 20 ASP cc_start: 0.7426 (m-30) cc_final: 0.7183 (m-30) REVERT: A 27 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7530 (mmt-90) REVERT: A 81 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7492 (ttm170) REVERT: A 217 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7982 (ttpm) REVERT: B 106 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: C 26 ASP cc_start: 0.7380 (p0) cc_final: 0.6776 (p0) REVERT: C 52 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6994 (mm-30) REVERT: C 76 THR cc_start: 0.7753 (m) cc_final: 0.7315 (p) REVERT: C 81 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7375 (ttm110) REVERT: C 142 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 209 ASP cc_start: 0.7086 (t0) cc_final: 0.6783 (t0) REVERT: F 227 LYS cc_start: 0.6785 (mttt) cc_final: 0.6428 (mptt) REVERT: I 67 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6914 (ttp-170) outliers start: 63 outliers final: 46 residues processed: 522 average time/residue: 0.7963 time to fit residues: 446.3497 Evaluate side-chains 544 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 495 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.164248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.155139 restraints weight = 22349.537| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.70 r_work: 0.4006 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15840 Z= 0.160 Angle : 0.577 10.467 21417 Z= 0.284 Chirality : 0.042 0.262 2412 Planarity : 0.004 0.041 2775 Dihedral : 4.293 51.557 2157 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.35 % Allowed : 34.76 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 2013 helix: 2.76 (0.16), residues: 981 sheet: -0.28 (0.26), residues: 420 loop : -1.07 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.012 0.001 TYR G 95 PHE 0.023 0.001 PHE A 123 TRP 0.031 0.001 TRP E 112 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00367 (15831) covalent geometry : angle 0.57616 (21399) SS BOND : bond 0.00439 ( 9) SS BOND : angle 1.29907 ( 18) hydrogen bonds : bond 0.03198 ( 912) hydrogen bonds : angle 3.78322 ( 2628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 511 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8038 (mm) cc_final: 0.7708 (tt) REVERT: A 20 ASP cc_start: 0.7417 (m-30) cc_final: 0.7189 (m-30) REVERT: A 27 ARG cc_start: 0.7798 (mmt-90) cc_final: 0.7318 (ttm170) REVERT: A 81 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7523 (ttm170) REVERT: A 217 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7982 (ttpm) REVERT: B 209 ASP cc_start: 0.7256 (t70) cc_final: 0.6842 (t70) REVERT: B 217 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7869 (ttpp) REVERT: C 26 ASP cc_start: 0.7419 (p0) cc_final: 0.6844 (p0) REVERT: C 52 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7046 (mm-30) REVERT: C 81 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7390 (ttm110) REVERT: C 142 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6846 (mt-10) REVERT: C 209 ASP cc_start: 0.7070 (t0) cc_final: 0.6781 (t0) REVERT: F 219 LYS cc_start: 0.8082 (mttt) cc_final: 0.7818 (mttp) REVERT: F 227 LYS cc_start: 0.6777 (mttt) cc_final: 0.6443 (mptt) REVERT: I 67 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6911 (ttp-170) outliers start: 54 outliers final: 47 residues processed: 529 average time/residue: 0.8035 time to fit residues: 456.7851 Evaluate side-chains 559 residues out of total 1611 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 510 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 224 GLU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.163826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.154712 restraints weight = 22176.392| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.69 r_work: 0.4001 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15840 Z= 0.174 Angle : 0.591 10.482 21417 Z= 0.291 Chirality : 0.042 0.210 2412 Planarity : 0.004 0.041 2775 Dihedral : 4.319 50.921 2157 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.41 % Allowed : 34.82 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2013 helix: 2.72 (0.16), residues: 981 sheet: -0.33 (0.26), residues: 420 loop : -1.09 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.011 0.001 TYR G 95 PHE 0.018 0.001 PHE A 123 TRP 0.030 0.002 TRP E 112 HIS 0.009 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00400 (15831) covalent geometry : angle 0.58963 (21399) SS BOND : bond 0.00485 ( 9) SS BOND : angle 1.30919 ( 18) hydrogen bonds : bond 0.03288 ( 912) hydrogen bonds : angle 3.82678 ( 2628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9055.40 seconds wall clock time: 154 minutes 3.90 seconds (9243.90 seconds total)