Starting phenix.real_space_refine on Wed Aug 5 06:53:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zzo_75011/08_2026/9zzo_75011.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zzo_75011/08_2026/9zzo_75011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zzo_75011/08_2026/9zzo_75011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zzo_75011/08_2026/9zzo_75011.map" model { file = "/net/cci-nas-00/data/ceres_data/9zzo_75011/08_2026/9zzo_75011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zzo_75011/08_2026/9zzo_75011.cif" } resolution = 2.6 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= 0.003 sd= 1.000 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: 6 Type Number sf(0) Gaussians I 1 10.91 5 P 8 5.49 5 S 31 5.16 5 C 5541 2.51 5 N 1430 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8637 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 820 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 109} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2686 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 325} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2027 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 5 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 4, 'TRP:plan': 1, 'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 62 Chain: "H" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1514 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1510 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 194} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'CVV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.18 Number of scatterers: 8637 At special positions: 0 Unit cell: (95.634, 105.57, 160.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 1 52.95 S 31 16.00 P 8 15.00 O 1626 8.00 N 1430 7.00 C 5541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 412.0 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 18 sheets defined 23.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'E' and resid 86 through 90 removed outlier: 4.108A pdb=" N THR E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'A' and resid 58 through 88 removed outlier: 3.571A pdb=" N TYR A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 122 removed outlier: 4.100A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 127 through 161 Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.520A pdb=" N ALA A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.532A pdb=" N ALA A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 266 through 299 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 306 through 333 Proline residue: A 327 - end of helix Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.601A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.962A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.509A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.576A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.673A pdb=" N GLY E 10 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 112 through 117 Processing sheet with id=AA4, first strand: chain 'C' and resid 26 through 28 removed outlier: 5.973A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 148 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 26 through 28 removed outlier: 5.973A pdb=" N PHE C 27 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 148 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS C 170 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N VAL C 142 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 140 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 188 removed outlier: 3.502A pdb=" N LEU C 199 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.959A pdb=" N TYR C 321 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C 343 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N VAL C 319 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 316 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 242 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE C 231 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU C 257 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE C 233 " --> pdb=" O MET C 255 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N MET C 255 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 235 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'H' and resid 14 through 15 removed outlier: 8.563A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.648A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.816A pdb=" N LYS H 153 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.816A pdb=" N LYS H 153 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 160 through 164 removed outlier: 4.057A pdb=" N VAL H 208 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL H 217 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.527A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.952A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.135A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 146 through 148 removed outlier: 3.915A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 3380 1.39 - 1.57: 5374 1.57 - 1.75: 29 1.75 - 1.93: 44 1.93 - 2.11: 1 Bond restraints: 8828 Sorted by residual: bond pdb=" C16 CVV A 401 " pdb=" C8 CVV A 401 " ideal model delta sigma weight residual 1.543 1.669 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" OG1 TPO A 381 " pdb=" P TPO A 381 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO A 380 " pdb=" P TPO A 380 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C9 CVV A 401 " pdb=" N1 CVV A 401 " ideal model delta sigma weight residual 1.344 1.451 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C5 PIO C 401 " pdb=" C6 PIO C 401 " ideal model delta sigma weight residual 1.532 1.621 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 8823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 11864 3.12 - 6.25: 153 6.25 - 9.37: 38 9.37 - 12.50: 11 12.50 - 15.62: 3 Bond angle restraints: 12069 Sorted by residual: angle pdb=" CA MET A 90 " pdb=" CB MET A 90 " pdb=" CG MET A 90 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" CB MET A 142 " pdb=" CG MET A 142 " pdb=" SD MET A 142 " ideal model delta sigma weight residual 112.70 128.32 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 127.96 -15.26 3.00e+00 1.11e-01 2.59e+01 angle pdb=" C VAL A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 122.13 114.34 7.79 1.85e+00 2.92e-01 1.77e+01 angle pdb=" CB TPO A 381 " pdb=" OG1 TPO A 381 " pdb=" P TPO A 381 " ideal model delta sigma weight residual 119.31 106.70 12.61 3.00e+00 1.11e-01 1.77e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4441 17.20 - 34.40: 577 34.40 - 51.60: 182 51.60 - 68.80: 32 68.80 - 86.00: 10 Dihedral angle restraints: 5242 sinusoidal: 1895 harmonic: 3347 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 43.87 49.13 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CA ILE A 237 " pdb=" C ILE A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA CYS A 161 " pdb=" C CYS A 161 " pdb=" N HIS A 162 " pdb=" CA HIS A 162 " ideal model delta harmonic sigma weight residual 180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1299 0.092 - 0.185: 131 0.185 - 0.277: 6 0.277 - 0.370: 3 0.370 - 0.462: 2 Chirality restraints: 1441 Sorted by residual: chirality pdb=" C4 CVV A 401 " pdb=" C3 CVV A 401 " pdb=" C5 CVV A 401 " pdb=" N2 CVV A 401 " both_signs ideal model delta sigma weight residual False 2.42 2.88 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" C25 CVV A 401 " pdb=" C24 CVV A 401 " pdb=" C26 CVV A 401 " pdb=" C27 CVV A 401 " both_signs ideal model delta sigma weight residual True 2.39 -2.80 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C16 CVV A 401 " pdb=" C17 CVV A 401 " pdb=" C8 CVV A 401 " pdb=" O3 CVV A 401 " both_signs ideal model delta sigma weight residual False 2.61 2.96 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1438 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 162 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO A 163 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 188 " -0.173 9.50e-02 1.11e+02 7.84e-02 4.96e+00 pdb=" NE ARG C 188 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 188 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 188 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 188 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 183 " 0.012 2.00e-02 2.50e+03 1.18e-02 3.48e+00 pdb=" CG TRP A 183 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 183 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 183 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 183 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 183 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 183 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 183 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 183 " 0.003 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2656 2.82 - 3.36: 7700 3.36 - 3.89: 14962 3.89 - 4.43: 16721 4.43 - 4.96: 29160 Nonbonded interactions: 71199 Sorted by model distance: nonbonded pdb=" OD1 ASP C 204 " pdb=" OH TYR C 208 " model vdw 2.289 3.040 nonbonded pdb=" O SER H 88 " pdb=" OG SER H 88 " model vdw 2.297 3.040 nonbonded pdb=" O ILE L 107 " pdb=" OH TYR L 141 " model vdw 2.298 3.040 nonbonded pdb=" O ALA A 104 " pdb=" ND2 ASN A 141 " model vdw 2.355 3.120 nonbonded pdb=" O SER E 84 " pdb=" OG SER E 84 " model vdw 2.355 3.040 ... (remaining 71194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.006 0.126 8833 Z= 0.286 Angle : 0.934 15.622 12079 Z= 0.425 Chirality : 0.053 0.462 1441 Planarity : 0.005 0.078 1499 Dihedral : 17.459 86.001 3067 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.17 % Allowed : 40.72 % Favored : 54.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.13 (0.25), residues: 1109 helix: -0.21 (0.31), residues: 244 sheet: 1.04 (0.28), residues: 382 loop : -0.91 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 188 TYR 0.031 0.001 TYR H 155 PHE 0.022 0.001 PHE L 140 TRP 0.031 0.001 TRP A 183 HIS 0.007 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.29 ( 8828) covalent geometry : angle 0.93390 / 0.43 (12069) SS BOND : bond 0.00126 / 0.07 ( 5) SS BOND : angle 0.35491 / 0.18 ( 10) hydrogen bonds : bond 0.19117 / 13.31 ( 416) hydrogen bonds : angle 8.11523 / 5.67 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.9036 (mtp85) REVERT: A 139 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: A 176 LYS cc_start: 0.8532 (mppt) cc_final: 0.8012 (mppt) outliers start: 46 outliers final: 42 residues processed: 329 average time/residue: 0.3037 time to fit residues: 109.9593 Evaluate side-chains 333 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 193 TYR Chi-restraints excluded: chain L residue 197 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 73 ASN C 83 ASN C 85 GLN C 130 GLN C 162 ASN C 248 GLN C 295 HIS A 95 ASN A 162 HIS H 165 ASN L 7 GLN L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.158947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116495 restraints weight = 10371.427| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.52 r_work: 0.3277 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8833 Z= 0.160 Angle : 0.631 8.659 12079 Z= 0.317 Chirality : 0.044 0.160 1441 Planarity : 0.004 0.050 1499 Dihedral : 8.283 67.735 1367 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 7.76 % Allowed : 35.88 % Favored : 56.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.18 (0.25), residues: 1109 helix: 0.75 (0.32), residues: 243 sheet: 0.84 (0.27), residues: 381 loop : -0.77 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 188 TYR 0.017 0.001 TYR H 107 PHE 0.015 0.001 PHE H 156 TRP 0.006 0.001 TRP H 113 HIS 0.003 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 8828) covalent geometry : angle 0.63139 / 0.32 (12069) SS BOND : bond 0.00221 / 0.11 ( 5) SS BOND : angle 0.70982 / 0.42 ( 10) hydrogen bonds : bond 0.03892 / 2.64 ( 416) hydrogen bonds : angle 5.54393 / 3.88 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 294 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 37 TYR cc_start: 0.9390 (m-80) cc_final: 0.9181 (m-80) REVERT: E 109 GLN cc_start: 0.9280 (tp-100) cc_final: 0.9056 (tp-100) REVERT: C 52 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8315 (mtt90) REVERT: C 200 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8113 (mp0) REVERT: C 232 LYS cc_start: 0.8664 (tttp) cc_final: 0.8418 (tttp) REVERT: C 314 ILE cc_start: 0.8248 (mp) cc_final: 0.8024 (mp) REVERT: A 139 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: A 147 PHE cc_start: 0.8476 (m-80) cc_final: 0.8002 (m-80) REVERT: A 176 LYS cc_start: 0.8615 (mppt) cc_final: 0.7959 (mppt) REVERT: H 186 TYR cc_start: 0.8684 (m-80) cc_final: 0.8064 (m-80) REVERT: H 189 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8103 (p) outliers start: 69 outliers final: 40 residues processed: 329 average time/residue: 0.3576 time to fit residues: 128.3662 Evaluate side-chains 322 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 193 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.0020 chunk 24 optimal weight: 0.0060 chunk 64 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 ASN C 130 GLN C 295 HIS A 162 HIS A 291 HIS H 165 ASN L 7 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.160182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117700 restraints weight = 10569.001| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.58 r_work: 0.3293 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8833 Z= 0.118 Angle : 0.603 8.526 12079 Z= 0.299 Chirality : 0.043 0.165 1441 Planarity : 0.004 0.035 1499 Dihedral : 7.168 69.135 1332 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 8.44 % Allowed : 34.87 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.24 (0.25), residues: 1109 helix: 0.98 (0.32), residues: 238 sheet: 0.78 (0.27), residues: 381 loop : -0.71 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 188 TYR 0.014 0.001 TYR A 66 PHE 0.014 0.001 PHE L 140 TRP 0.015 0.001 TRP A 183 HIS 0.002 0.000 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8828) covalent geometry : angle 0.60281 / 0.30 (12069) SS BOND : bond 0.00142 / 0.08 ( 5) SS BOND : angle 0.51274 / 0.27 ( 10) hydrogen bonds : bond 0.03598 / 2.43 ( 416) hydrogen bonds : angle 5.15699 / 3.62 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 284 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 109 GLN cc_start: 0.9246 (tp-100) cc_final: 0.8995 (tp-100) REVERT: C 52 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8259 (mtt90) REVERT: C 99 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8377 (mmm160) REVERT: C 200 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8135 (mp0) REVERT: C 232 LYS cc_start: 0.8715 (tttp) cc_final: 0.8472 (tttp) REVERT: C 270 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8507 (tttp) REVERT: C 344 MET cc_start: 0.9350 (mtp) cc_final: 0.9117 (mtp) REVERT: A 139 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: A 147 PHE cc_start: 0.8438 (m-80) cc_final: 0.8053 (m-80) REVERT: A 176 LYS cc_start: 0.8699 (mppt) cc_final: 0.8377 (mppt) REVERT: A 249 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7087 (tmm) REVERT: H 127 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7822 (pptt) outliers start: 75 outliers final: 38 residues processed: 321 average time/residue: 0.3744 time to fit residues: 131.3366 Evaluate side-chains 317 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 73 ASN C 83 ASN C 295 HIS ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 179 ASN H 165 ASN L 7 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.155859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112660 restraints weight = 10244.842| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.49 r_work: 0.3231 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8833 Z= 0.183 Angle : 0.639 9.449 12079 Z= 0.319 Chirality : 0.044 0.200 1441 Planarity : 0.004 0.042 1499 Dihedral : 7.051 65.853 1327 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 7.31 % Allowed : 36.00 % Favored : 56.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.07 (0.25), residues: 1109 helix: 0.89 (0.31), residues: 243 sheet: 0.52 (0.27), residues: 375 loop : -0.70 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 188 TYR 0.017 0.002 TYR H 107 PHE 0.020 0.002 PHE H 156 TRP 0.024 0.002 TRP A 183 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 8828) covalent geometry : angle 0.63881 / 0.32 (12069) SS BOND : bond 0.00146 / 0.08 ( 5) SS BOND : angle 0.86478 / 0.47 ( 10) hydrogen bonds : bond 0.03612 / 2.47 ( 416) hydrogen bonds : angle 5.08486 / 3.58 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 109 GLN cc_start: 0.9289 (tp-100) cc_final: 0.9077 (tp-100) REVERT: C 232 LYS cc_start: 0.8795 (tttp) cc_final: 0.8580 (tttp) REVERT: C 270 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8134 (ttpt) REVERT: A 139 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: A 147 PHE cc_start: 0.8395 (m-80) cc_final: 0.8043 (m-80) REVERT: A 249 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7108 (tmm) REVERT: L 10 SER cc_start: 0.9252 (m) cc_final: 0.8913 (p) outliers start: 65 outliers final: 42 residues processed: 318 average time/residue: 0.3367 time to fit residues: 116.3282 Evaluate side-chains 322 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 30 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS A 179 ASN H 165 ASN L 7 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.151380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108390 restraints weight = 10047.885| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.41 r_work: 0.3172 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8833 Z= 0.256 Angle : 0.685 9.975 12079 Z= 0.348 Chirality : 0.046 0.182 1441 Planarity : 0.005 0.053 1499 Dihedral : 7.236 62.995 1322 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 9.45 % Allowed : 33.97 % Favored : 56.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.20 (0.25), residues: 1109 helix: 0.59 (0.31), residues: 244 sheet: 0.26 (0.27), residues: 376 loop : -0.74 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 188 TYR 0.026 0.002 TYR H 155 PHE 0.029 0.002 PHE H 156 TRP 0.019 0.002 TRP A 183 HIS 0.004 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.26 ( 8828) covalent geometry : angle 0.68468 / 0.35 (12069) SS BOND : bond 0.00224 / 0.11 ( 5) SS BOND : angle 0.92949 / 0.53 ( 10) hydrogen bonds : bond 0.03933 / 2.72 ( 416) hydrogen bonds : angle 5.28459 / 3.71 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 276 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 LEU cc_start: 0.9321 (mp) cc_final: 0.9025 (mt) REVERT: E 89 ASP cc_start: 0.9224 (m-30) cc_final: 0.8925 (m-30) REVERT: E 109 GLN cc_start: 0.9316 (tp-100) cc_final: 0.9072 (tp-100) REVERT: C 161 ARG cc_start: 0.8782 (pmt170) cc_final: 0.8568 (ptt-90) REVERT: C 236 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8297 (mtp85) REVERT: C 257 GLU cc_start: 0.7912 (tp30) cc_final: 0.7616 (tp30) REVERT: C 270 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8126 (ttpt) REVERT: C 299 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9233 (p0) REVERT: C 344 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.9113 (mtm) REVERT: A 139 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: A 147 PHE cc_start: 0.8339 (m-80) cc_final: 0.8013 (m-80) REVERT: A 235 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: A 249 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7015 (tmm) REVERT: H 127 LYS cc_start: 0.8614 (pptt) cc_final: 0.8282 (pptt) REVERT: L 5 MET cc_start: 0.9052 (tpt) cc_final: 0.8831 (tpt) REVERT: L 10 SER cc_start: 0.9203 (m) cc_final: 0.8903 (p) outliers start: 84 outliers final: 50 residues processed: 326 average time/residue: 0.3191 time to fit residues: 113.9469 Evaluate side-chains 325 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 163 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 248 GLN A 162 HIS H 165 ASN L 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110344 restraints weight = 10387.522| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.48 r_work: 0.3197 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8833 Z= 0.151 Angle : 0.643 9.066 12079 Z= 0.321 Chirality : 0.044 0.220 1441 Planarity : 0.004 0.043 1499 Dihedral : 7.064 65.563 1322 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.09 % Allowed : 37.35 % Favored : 55.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.10 (0.25), residues: 1109 helix: 0.78 (0.31), residues: 244 sheet: 0.28 (0.27), residues: 370 loop : -0.69 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 188 TYR 0.025 0.002 TYR H 155 PHE 0.019 0.001 PHE H 156 TRP 0.026 0.002 TRP A 183 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8828) covalent geometry : angle 0.64278 / 0.32 (12069) SS BOND : bond 0.00170 / 0.09 ( 5) SS BOND : angle 0.61459 / 0.36 ( 10) hydrogen bonds : bond 0.03683 / 2.52 ( 416) hydrogen bonds : angle 5.09195 / 3.60 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 37 TYR cc_start: 0.9405 (m-80) cc_final: 0.9028 (m-80) REVERT: E 89 ASP cc_start: 0.9216 (m-30) cc_final: 0.8868 (m-30) REVERT: E 109 GLN cc_start: 0.9300 (tp-100) cc_final: 0.9059 (tp-100) REVERT: C 161 ARG cc_start: 0.8754 (pmt170) cc_final: 0.8458 (ptt-90) REVERT: C 257 GLU cc_start: 0.7864 (tp30) cc_final: 0.7594 (tp30) REVERT: C 270 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8569 (tttp) REVERT: C 299 ASN cc_start: 0.9453 (OUTLIER) cc_final: 0.9217 (p0) REVERT: C 344 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9070 (mtm) REVERT: A 77 ASN cc_start: 0.7365 (m110) cc_final: 0.7130 (m110) REVERT: A 139 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: A 147 PHE cc_start: 0.8367 (m-80) cc_final: 0.8023 (m-80) REVERT: A 235 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6765 (m-10) REVERT: A 249 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.6928 (tmm) REVERT: H 134 LEU cc_start: 0.8514 (mp) cc_final: 0.8239 (mp) REVERT: L 10 SER cc_start: 0.9207 (m) cc_final: 0.8911 (p) outliers start: 63 outliers final: 38 residues processed: 321 average time/residue: 0.3504 time to fit residues: 122.9087 Evaluate side-chains 322 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 270 LYS Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 0.0570 chunk 23 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 ASN C 295 HIS A 162 HIS H 42 GLN H 165 ASN L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111107 restraints weight = 10212.583| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.46 r_work: 0.3209 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8833 Z= 0.141 Angle : 0.647 10.228 12079 Z= 0.321 Chirality : 0.044 0.232 1441 Planarity : 0.004 0.048 1499 Dihedral : 6.913 66.978 1320 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.76 % Allowed : 36.45 % Favored : 55.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.01 (0.25), residues: 1109 helix: 0.89 (0.32), residues: 244 sheet: 0.36 (0.27), residues: 370 loop : -0.65 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 188 TYR 0.022 0.001 TYR A 140 PHE 0.017 0.001 PHE H 156 TRP 0.020 0.001 TRP A 183 HIS 0.002 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8828) covalent geometry : angle 0.64677 / 0.32 (12069) SS BOND : bond 0.00193 / 0.10 ( 5) SS BOND : angle 0.60808 / 0.35 ( 10) hydrogen bonds : bond 0.03595 / 2.46 ( 416) hydrogen bonds : angle 4.97723 / 3.52 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 283 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 37 TYR cc_start: 0.9423 (m-80) cc_final: 0.9072 (m-80) REVERT: E 89 ASP cc_start: 0.9223 (m-30) cc_final: 0.8883 (m-30) REVERT: C 75 PHE cc_start: 0.8241 (m-80) cc_final: 0.7455 (m-80) REVERT: C 161 ARG cc_start: 0.8768 (pmt170) cc_final: 0.8475 (ptt-90) REVERT: C 236 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8304 (mtp85) REVERT: C 257 GLU cc_start: 0.7920 (tp30) cc_final: 0.7605 (tp30) REVERT: C 344 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9056 (mtm) REVERT: A 77 ASN cc_start: 0.7306 (m110) cc_final: 0.7101 (m110) REVERT: A 139 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: A 147 PHE cc_start: 0.8302 (m-80) cc_final: 0.7989 (m-80) REVERT: A 235 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: A 249 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7054 (tmm) REVERT: H 127 LYS cc_start: 0.8578 (pptt) cc_final: 0.8319 (pptt) REVERT: H 134 LEU cc_start: 0.8522 (mp) cc_final: 0.8248 (mp) REVERT: L 10 SER cc_start: 0.9183 (m) cc_final: 0.8884 (p) REVERT: L 25 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7868 (mmm160) outliers start: 69 outliers final: 44 residues processed: 320 average time/residue: 0.3534 time to fit residues: 123.7412 Evaluate side-chains 326 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 73 ASN C 295 HIS A 162 HIS H 165 ASN L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108651 restraints weight = 9844.893| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.40 r_work: 0.3171 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8833 Z= 0.214 Angle : 0.692 11.712 12079 Z= 0.345 Chirality : 0.045 0.230 1441 Planarity : 0.005 0.054 1499 Dihedral : 7.034 64.287 1320 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 7.99 % Allowed : 37.12 % Favored : 54.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.11 (0.25), residues: 1109 helix: 0.71 (0.31), residues: 244 sheet: 0.27 (0.27), residues: 368 loop : -0.65 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 188 TYR 0.019 0.002 TYR A 140 PHE 0.024 0.002 PHE H 156 TRP 0.016 0.002 TRP A 183 HIS 0.004 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 8828) covalent geometry : angle 0.69174 / 0.35 (12069) SS BOND : bond 0.00216 / 0.11 ( 5) SS BOND : angle 0.76869 / 0.45 ( 10) hydrogen bonds : bond 0.03833 / 2.62 ( 416) hydrogen bonds : angle 5.15187 / 3.64 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 LEU cc_start: 0.9299 (mp) cc_final: 0.8993 (mt) REVERT: E 89 ASP cc_start: 0.9218 (m-30) cc_final: 0.8874 (m-30) REVERT: C 161 ARG cc_start: 0.8798 (pmt170) cc_final: 0.8510 (ptt-90) REVERT: C 236 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8335 (mtp85) REVERT: C 257 GLU cc_start: 0.8018 (tp30) cc_final: 0.7703 (tp30) REVERT: C 344 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9087 (mtm) REVERT: A 77 ASN cc_start: 0.7460 (m110) cc_final: 0.7247 (m110) REVERT: A 139 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: A 147 PHE cc_start: 0.8277 (m-80) cc_final: 0.7980 (m-80) REVERT: A 227 LYS cc_start: 0.8574 (mppt) cc_final: 0.8352 (mtmm) REVERT: A 235 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7111 (m-10) REVERT: A 249 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7247 (tmm) REVERT: H 127 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8331 (pptt) REVERT: H 134 LEU cc_start: 0.8639 (mp) cc_final: 0.8377 (mp) REVERT: L 5 MET cc_start: 0.9038 (tpt) cc_final: 0.8801 (tpt) REVERT: L 10 SER cc_start: 0.9206 (m) cc_final: 0.8920 (p) REVERT: L 25 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7938 (mmm160) outliers start: 71 outliers final: 53 residues processed: 321 average time/residue: 0.3237 time to fit residues: 113.6230 Evaluate side-chains 329 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 210 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 105 optimal weight: 0.0030 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 295 HIS A 162 HIS H 165 ASN L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111510 restraints weight = 9584.075| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.38 r_work: 0.3216 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8833 Z= 0.133 Angle : 0.672 12.601 12079 Z= 0.332 Chirality : 0.044 0.247 1441 Planarity : 0.004 0.051 1499 Dihedral : 6.884 67.202 1320 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.64 % Allowed : 38.02 % Favored : 55.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.01 (0.25), residues: 1109 helix: 0.84 (0.32), residues: 244 sheet: 0.37 (0.27), residues: 370 loop : -0.67 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 188 TYR 0.020 0.001 TYR A 140 PHE 0.019 0.001 PHE L 140 TRP 0.014 0.001 TRP A 183 HIS 0.002 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8828) covalent geometry : angle 0.67235 / 0.33 (12069) SS BOND : bond 0.00216 / 0.11 ( 5) SS BOND : angle 0.59243 / 0.34 ( 10) hydrogen bonds : bond 0.03635 / 2.45 ( 416) hydrogen bonds : angle 4.94494 / 3.52 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 283 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: E 59 TYR cc_start: 0.9212 (m-80) cc_final: 0.8909 (m-80) REVERT: E 89 ASP cc_start: 0.9226 (m-30) cc_final: 0.8894 (m-30) REVERT: C 71 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5697 (mt) REVERT: C 130 GLN cc_start: 0.8580 (tt0) cc_final: 0.8364 (tt0) REVERT: C 161 ARG cc_start: 0.8765 (pmt170) cc_final: 0.8479 (ptt-90) REVERT: C 232 LYS cc_start: 0.9013 (tttt) cc_final: 0.8331 (tttp) REVERT: C 236 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8300 (mtp85) REVERT: C 257 GLU cc_start: 0.7996 (tp30) cc_final: 0.7250 (tp30) REVERT: C 344 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9057 (mtm) REVERT: A 139 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: A 147 PHE cc_start: 0.8300 (m-80) cc_final: 0.7986 (m-80) REVERT: A 235 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: A 249 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7301 (tmm) REVERT: H 127 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8306 (pptt) REVERT: H 134 LEU cc_start: 0.8584 (mp) cc_final: 0.8331 (mp) REVERT: H 209 ASN cc_start: 0.8101 (m-40) cc_final: 0.7106 (p0) REVERT: L 10 SER cc_start: 0.9192 (m) cc_final: 0.8900 (p) REVERT: L 25 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7896 (mmm160) outliers start: 59 outliers final: 44 residues processed: 315 average time/residue: 0.3366 time to fit residues: 116.4314 Evaluate side-chains 331 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 5 GLN A 162 HIS H 165 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110871 restraints weight = 9791.632| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.40 r_work: 0.3204 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8833 Z= 0.152 Angle : 0.704 14.298 12079 Z= 0.344 Chirality : 0.045 0.248 1441 Planarity : 0.004 0.054 1499 Dihedral : 6.835 67.177 1320 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.07 % Allowed : 39.37 % Favored : 54.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.04 (0.25), residues: 1109 helix: 0.69 (0.31), residues: 244 sheet: 0.41 (0.27), residues: 370 loop : -0.65 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 188 TYR 0.029 0.001 TYR A 66 PHE 0.018 0.001 PHE L 140 TRP 0.014 0.001 TRP A 183 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 8828) covalent geometry : angle 0.70377 / 0.34 (12069) SS BOND : bond 0.00230 / 0.12 ( 5) SS BOND : angle 0.65537 / 0.38 ( 10) hydrogen bonds : bond 0.03678 / 2.48 ( 416) hydrogen bonds : angle 5.02083 / 3.57 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: E 89 ASP cc_start: 0.9208 (m-30) cc_final: 0.8861 (m-30) REVERT: C 71 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5712 (mt) REVERT: C 99 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8406 (tpm-80) REVERT: C 232 LYS cc_start: 0.9025 (tttt) cc_final: 0.8332 (ttmt) REVERT: C 236 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8283 (mtp85) REVERT: C 257 GLU cc_start: 0.8030 (tp30) cc_final: 0.7500 (tp30) REVERT: C 344 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9051 (mtm) REVERT: A 139 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: A 147 PHE cc_start: 0.8305 (m-80) cc_final: 0.8001 (m-80) REVERT: A 227 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8494 (mppt) REVERT: A 235 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.7088 (m-10) REVERT: A 249 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7304 (tmm) REVERT: H 127 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (pptt) REVERT: H 134 LEU cc_start: 0.8607 (mp) cc_final: 0.8340 (mp) REVERT: H 209 ASN cc_start: 0.7934 (m-40) cc_final: 0.6867 (p0) REVERT: L 10 SER cc_start: 0.9196 (m) cc_final: 0.8905 (p) REVERT: L 25 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7928 (mmm160) outliers start: 54 outliers final: 41 residues processed: 311 average time/residue: 0.3779 time to fit residues: 128.4526 Evaluate side-chains 335 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 ARG Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 101 ARG Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 127 LYS Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 5 GLN C 295 HIS A 162 HIS H 165 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111478 restraints weight = 10000.403| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.44 r_work: 0.3213 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8833 Z= 0.142 Angle : 0.697 14.032 12079 Z= 0.340 Chirality : 0.045 0.253 1441 Planarity : 0.004 0.052 1499 Dihedral : 6.786 67.530 1320 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.74 % Allowed : 39.60 % Favored : 54.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.00 (0.25), residues: 1109 helix: 0.73 (0.32), residues: 244 sheet: 0.47 (0.27), residues: 369 loop : -0.67 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 188 TYR 0.021 0.001 TYR A 66 PHE 0.018 0.001 PHE E 29 TRP 0.014 0.001 TRP A 183 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 8828) covalent geometry : angle 0.69720 / 0.34 (12069) SS BOND : bond 0.00231 / 0.12 ( 5) SS BOND : angle 0.63282 / 0.37 ( 10) hydrogen bonds : bond 0.03609 / 2.44 ( 416) hydrogen bonds : angle 4.95803 / 3.53 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4305.47 seconds wall clock time: 73 minutes 46.34 seconds (4426.34 seconds total)