Starting phenix.real_space_refine on Wed Aug 5 00:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oko_70570/08_2026/9oko_70570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oko_70570/08_2026/9oko_70570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oko_70570/08_2026/9oko_70570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oko_70570/08_2026/9oko_70570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oko_70570/08_2026/9oko_70570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oko_70570/08_2026/9oko_70570.map" } resolution = 2.5 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= 0.008 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 62 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 4984 2.51 5 N 1334 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 7730 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1940 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain: "D" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1889 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 13, 'TRANS': 229} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ANP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5416 SG CYS D 199 51.764 34.570 80.565 1.00 84.78 S ATOM 5366 SG CYS D 193 47.339 34.114 81.986 1.00 87.05 S ATOM 5422 SG CYS D 200 48.382 32.975 85.600 1.00 83.52 S Restraints were copied for chains: C, E Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7730 At special positions: 0 Unit cell: (71.3952, 82.0512, 109.757, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 48 16.00 P 6 15.00 Mg 2 11.99 O 1352 8.00 N 1334 7.00 C 4984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.39 Conformation dependent library (CDL) restraints added in 384.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 236 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 234 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 197 " pdb="ZN ZN D 303 " - pdb=" SG CYS D 199 " pdb=" ZN D 304 " pdb="ZN ZN D 304 " - pdb=" NE2 HIS D 232 " pdb="ZN ZN D 304 " - pdb=" ND1 HIS D 230 " pdb="ZN ZN D 304 " - pdb=" SG CYS D 200 " pdb="ZN ZN D 304 " - pdb=" SG CYS D 193 " pdb=" ZN E 303 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 236 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 234 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 197 " pdb="ZN ZN E 303 " - pdb=" SG CYS E 199 " pdb=" ZN E 304 " pdb="ZN ZN E 304 " - pdb=" NE2 HIS E 232 " pdb="ZN ZN E 304 " - pdb=" ND1 HIS E 230 " pdb="ZN ZN E 304 " - pdb=" SG CYS E 193 " pdb="ZN ZN E 304 " - pdb=" SG CYS E 200 " Number of angles added : 8 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 64.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 removed outlier: 3.515A pdb=" N LEU B 5 " --> pdb=" O MET B 1 " (cutoff:3.500A) Proline residue: B 7 - end of helix removed outlier: 3.649A pdb=" N CYS B 17 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 41 through 53 removed outlier: 4.107A pdb=" N GLY B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 76 Processing helix chain 'B' and resid 81 through 104 removed outlier: 5.044A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 164 through 184 Processing helix chain 'B' and resid 191 through 205 Proline residue: B 199 - end of helix removed outlier: 4.190A pdb=" N ARG B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 236 Processing helix chain 'B' and resid 238 through 256 removed outlier: 3.575A pdb=" N MET B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 30 Proline residue: C 7 - end of helix removed outlier: 3.649A pdb=" N CYS C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 31 through 41 Processing helix chain 'C' and resid 41 through 53 removed outlier: 4.106A pdb=" N GLY C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 76 Processing helix chain 'C' and resid 81 through 104 removed outlier: 5.045A pdb=" N LEU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER C 95 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'C' and resid 123 through 144 Processing helix chain 'C' and resid 144 through 154 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 164 through 184 Processing helix chain 'C' and resid 191 through 205 Proline residue: C 199 - end of helix removed outlier: 4.190A pdb=" N ARG C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 236 Processing helix chain 'C' and resid 238 through 256 removed outlier: 3.575A pdb=" N MET C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.593A pdb=" N ALA D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.776A pdb=" N ILE D 114 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.523A pdb=" N LYS D 120 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 152 through 171 Processing helix chain 'D' and resid 212 through 224 Proline residue: D 219 - end of helix removed outlier: 3.845A pdb=" N GLU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.593A pdb=" N ALA E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.777A pdb=" N ILE E 114 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.522A pdb=" N LYS E 120 " --> pdb=" O PRO E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 152 through 171 Processing helix chain 'E' and resid 212 through 224 Proline residue: E 219 - end of helix removed outlier: 3.844A pdb=" N GLU E 223 " --> pdb=" O PRO E 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 27 removed outlier: 6.476A pdb=" N VAL D 19 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER D 13 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER D 21 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER D 11 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL D 23 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 5 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL D 10 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU D 58 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.718A pdb=" N LEU D 142 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL D 177 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU D 144 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 33 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 32 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU D 192 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR D 34 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU D 194 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 36 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS D 200 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 183 through 185 Processing sheet with id=AA4, first strand: chain 'D' and resid 235 through 236 removed outlier: 4.314A pdb=" N ARG D 235 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 17 through 27 removed outlier: 6.476A pdb=" N VAL E 19 " --> pdb=" O SER E 13 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N SER E 13 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER E 21 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER E 11 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL E 23 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 5 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL E 10 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU E 58 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.718A pdb=" N LEU E 142 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL E 177 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU E 144 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU E 33 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE E 32 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU E 192 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR E 34 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU E 194 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 36 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS E 200 " --> pdb=" O CYS E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 185 Processing sheet with id=AA8, first strand: chain 'E' and resid 235 through 236 removed outlier: 4.314A pdb=" N ARG E 235 " --> pdb=" O VAL E 243 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1362 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: 0.86 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2492 1.34 - 1.46: 1337 1.46 - 1.58: 3940 1.58 - 1.69: 9 1.69 - 1.81: 84 Bond restraints: 7862 Sorted by residual: bond pdb=" O3A ANP E 301 " pdb=" PB ANP E 301 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 5.01e+01 bond pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" N3B ANP E 301 " pdb=" PG ANP E 301 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.84e+01 bond pdb=" O5' ANP D 301 " pdb=" PA ANP D 301 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.54e+01 ... (remaining 7857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 10603 3.05 - 6.10: 89 6.10 - 9.15: 8 9.15 - 12.20: 2 12.20 - 15.25: 2 Bond angle restraints: 10704 Sorted by residual: angle pdb=" PB ANP D 301 " pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " ideal model delta sigma weight residual 126.95 111.70 15.25 3.00e+00 1.11e-01 2.58e+01 angle pdb=" PB ANP E 301 " pdb=" N3B ANP E 301 " pdb=" PG ANP E 301 " ideal model delta sigma weight residual 126.95 111.73 15.22 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O1B ANP E 301 " pdb=" PB ANP E 301 " pdb=" O2B ANP E 301 " ideal model delta sigma weight residual 120.08 110.13 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O1B ANP D 301 " pdb=" PB ANP D 301 " pdb=" O2B ANP D 301 " ideal model delta sigma weight residual 120.08 110.16 9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N GLY E 65 " pdb=" CA GLY E 65 " pdb=" C GLY E 65 " ideal model delta sigma weight residual 111.67 114.53 -2.86 9.20e-01 1.18e+00 9.69e+00 ... (remaining 10699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 4363 17.01 - 34.01: 277 34.01 - 51.02: 56 51.02 - 68.02: 36 68.02 - 85.03: 16 Dihedral angle restraints: 4748 sinusoidal: 1886 harmonic: 2862 Sorted by residual: dihedral pdb=" O1B ANP D 301 " pdb=" N3B ANP D 301 " pdb=" PB ANP D 301 " pdb=" PG ANP D 301 " ideal model delta sinusoidal sigma weight residual 35.15 120.18 -85.03 1 3.00e+01 1.11e-03 9.74e+00 dihedral pdb=" O1B ANP E 301 " pdb=" N3B ANP E 301 " pdb=" PB ANP E 301 " pdb=" PG ANP E 301 " ideal model delta sinusoidal sigma weight residual 35.15 120.16 -85.01 1 3.00e+01 1.11e-03 9.74e+00 dihedral pdb=" CB LYS B 258 " pdb=" CG LYS B 258 " pdb=" CD LYS B 258 " pdb=" CE LYS B 258 " ideal model delta sinusoidal sigma weight residual -180.00 -123.67 -56.33 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1024 0.053 - 0.107: 268 0.107 - 0.160: 28 0.160 - 0.213: 0 0.213 - 0.266: 2 Chirality restraints: 1322 Sorted by residual: chirality pdb=" C3' ANP E 301 " pdb=" C2' ANP E 301 " pdb=" C4' ANP E 301 " pdb=" O3' ANP E 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C3' ANP D 301 " pdb=" C2' ANP D 301 " pdb=" C4' ANP D 301 " pdb=" O3' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE D 114 " pdb=" CA ILE D 114 " pdb=" CG1 ILE D 114 " pdb=" CG2 ILE D 114 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1319 not shown) Planarity restraints: 1318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 160 " -0.016 2.00e-02 2.50e+03 1.38e-02 3.82e+00 pdb=" CG TYR E 160 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 160 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR E 160 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 160 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 160 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 160 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 160 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 160 " 0.016 2.00e-02 2.50e+03 1.36e-02 3.72e+00 pdb=" CG TYR D 160 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 160 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 160 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 160 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 160 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 160 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 160 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 123 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 124 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.024 5.00e-02 4.00e+02 ... (remaining 1315 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 25 2.44 - 3.05: 4698 3.05 - 3.67: 10874 3.67 - 4.28: 16429 4.28 - 4.90: 28095 Nonbonded interactions: 60121 Sorted by model distance: nonbonded pdb=" O3G ANP D 301 " pdb="MG MG D 302 " model vdw 1.823 2.170 nonbonded pdb=" O3G ANP E 301 " pdb="MG MG E 302 " model vdw 1.823 2.170 nonbonded pdb=" O2B ANP E 301 " pdb=" O3G ANP E 301 " model vdw 1.969 3.040 nonbonded pdb=" O2B ANP D 301 " pdb=" O3G ANP D 301 " model vdw 1.969 3.040 nonbonded pdb=" OG SER D 44 " pdb="MG MG D 302 " model vdw 2.031 2.170 ... (remaining 60116 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.420 Find NCS groups from input model: 0.060 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:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 0.142 7878 Z= 0.272 Angle : 0.765 15.252 10712 Z= 0.378 Chirality : 0.046 0.266 1322 Planarity : 0.005 0.043 1318 Dihedral : 14.162 85.030 2904 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.27), residues: 998 helix: 1.79 (0.22), residues: 584 sheet: 1.17 (0.60), residues: 64 loop : -0.83 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 205 TYR 0.034 0.003 TYR E 160 PHE 0.018 0.002 PHE B 57 TRP 0.013 0.002 TRP B 73 HIS 0.007 0.002 HIS D 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 ( 7862) covalent geometry : angle 0.76383 / 0.38 (10704) hydrogen bonds : bond 0.13015 / 7.86 ( 458) hydrogen bonds : angle 5.60424 / 3.93 ( 1362) metal coordination : bond 0.01088 / 0.72 ( 16) metal coordination : angle 1.41148 / 0.73 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 67 LEU cc_start: 0.9073 (tp) cc_final: 0.8844 (tp) REVERT: B 73 TRP cc_start: 0.8290 (t60) cc_final: 0.7972 (t60) REVERT: C 126 ASP cc_start: 0.7904 (m-30) cc_final: 0.7702 (m-30) REVERT: D 62 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7811 (tmtm) REVERT: D 87 ASN cc_start: 0.8649 (t0) cc_final: 0.8341 (t0) REVERT: D 100 ASP cc_start: 0.8557 (m-30) cc_final: 0.8282 (m-30) REVERT: D 171 ASP cc_start: 0.8815 (t70) cc_final: 0.8092 (t0) REVERT: E 87 ASN cc_start: 0.8378 (t0) cc_final: 0.8129 (t0) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.6927 time to fit residues: 150.3008 Evaluate side-chains 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 GLN D 64 ASN D 137 ASN D 165 GLN E 9 ASN E 64 ASN E 137 ASN E 165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.082375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.061239 restraints weight = 12375.627| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.73 r_work: 0.2529 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7878 Z= 0.132 Angle : 0.558 6.567 10712 Z= 0.276 Chirality : 0.040 0.147 1322 Planarity : 0.004 0.039 1318 Dihedral : 8.516 59.313 1136 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.27 % Allowed : 9.55 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.28), residues: 998 helix: 2.41 (0.22), residues: 592 sheet: 1.04 (0.64), residues: 66 loop : -0.56 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 77 TYR 0.011 0.001 TYR D 160 PHE 0.015 0.001 PHE C 57 TRP 0.015 0.001 TRP C 73 HIS 0.002 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7862) covalent geometry : angle 0.55771 / 0.28 (10704) hydrogen bonds : bond 0.04913 / 3.27 ( 458) hydrogen bonds : angle 4.27130 / 3.03 ( 1362) metal coordination : bond 0.00666 / 0.40 ( 16) metal coordination : angle 0.70171 / 0.33 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 256 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: C 4 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9176 (mm) REVERT: C 73 TRP cc_start: 0.8406 (t60) cc_final: 0.8182 (t60) REVERT: C 77 ARG cc_start: 0.7062 (mmp80) cc_final: 0.6827 (mmp80) REVERT: C 89 MET cc_start: 0.8710 (mtp) cc_final: 0.8491 (mtm) REVERT: C 256 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7413 (mpp) REVERT: D 62 LYS cc_start: 0.8411 (mtmm) cc_final: 0.7438 (tmtm) REVERT: D 137 ASN cc_start: 0.8128 (t0) cc_final: 0.7664 (t0) REVERT: D 241 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7509 (mtm-85) REVERT: E 62 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7364 (tmtm) REVERT: E 137 ASN cc_start: 0.8330 (t0) cc_final: 0.7863 (t0) REVERT: E 241 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7164 (mtm-85) outliers start: 19 outliers final: 4 residues processed: 148 average time/residue: 0.7214 time to fit residues: 111.5785 Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain E residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 97 optimal weight: 0.0170 chunk 16 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.061793 restraints weight = 12312.364| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.63 r_work: 0.2541 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7878 Z= 0.112 Angle : 0.514 6.122 10712 Z= 0.256 Chirality : 0.039 0.145 1322 Planarity : 0.004 0.041 1318 Dihedral : 5.840 55.296 1136 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.67 % Allowed : 11.93 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.30 (0.28), residues: 998 helix: 2.73 (0.23), residues: 576 sheet: 1.20 (0.64), residues: 66 loop : -0.48 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 138 TYR 0.010 0.001 TYR C 114 PHE 0.015 0.001 PHE C 57 TRP 0.016 0.001 TRP B 73 HIS 0.001 0.000 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7862) covalent geometry : angle 0.51438 / 0.26 (10704) hydrogen bonds : bond 0.04126 / 2.74 ( 458) hydrogen bonds : angle 3.93684 / 2.80 ( 1362) metal coordination : bond 0.00429 / 0.24 ( 16) metal coordination : angle 0.33885 / 0.19 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8526 (mtmm) cc_final: 0.7560 (tmtm) REVERT: D 91 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8179 (mmm-85) REVERT: D 137 ASN cc_start: 0.8262 (t0) cc_final: 0.7851 (t0) REVERT: E 62 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7454 (tmtm) REVERT: E 137 ASN cc_start: 0.8422 (t0) cc_final: 0.8005 (t0) REVERT: E 241 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7414 (mtm-85) outliers start: 14 outliers final: 2 residues processed: 137 average time/residue: 0.6554 time to fit residues: 93.6021 Evaluate side-chains 127 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN D 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.061838 restraints weight = 12584.309| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.66 r_work: 0.2548 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7878 Z= 0.107 Angle : 0.508 8.259 10712 Z= 0.252 Chirality : 0.039 0.207 1322 Planarity : 0.004 0.042 1318 Dihedral : 5.308 54.438 1136 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.55 % Allowed : 12.89 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.28), residues: 998 helix: 2.88 (0.22), residues: 576 sheet: 1.39 (0.66), residues: 66 loop : -0.52 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 138 TYR 0.007 0.001 TYR C 114 PHE 0.013 0.001 PHE C 57 TRP 0.018 0.001 TRP C 73 HIS 0.001 0.000 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7862) covalent geometry : angle 0.50857 / 0.25 (10704) hydrogen bonds : bond 0.03895 / 2.60 ( 458) hydrogen bonds : angle 3.84167 / 2.72 ( 1362) metal coordination : bond 0.00398 / 0.20 ( 16) metal coordination : angle 0.31939 / 0.18 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.250 Fit side-chains REVERT: B 256 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7607 (mpp) REVERT: D 62 LYS cc_start: 0.8481 (mtmm) cc_final: 0.7571 (tmtm) REVERT: D 137 ASN cc_start: 0.8211 (t0) cc_final: 0.7826 (t0) REVERT: E 1 MET cc_start: 0.7496 (tmm) cc_final: 0.6959 (pmm) REVERT: E 62 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8019 (mttt) REVERT: E 137 ASN cc_start: 0.8348 (t0) cc_final: 0.7970 (t0) outliers start: 13 outliers final: 2 residues processed: 136 average time/residue: 0.7698 time to fit residues: 109.0945 Evaluate side-chains 131 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain D residue 237 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.060879 restraints weight = 12583.015| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.66 r_work: 0.2528 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7878 Z= 0.121 Angle : 0.521 8.353 10712 Z= 0.259 Chirality : 0.039 0.170 1322 Planarity : 0.004 0.043 1318 Dihedral : 5.258 56.556 1136 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.67 % Allowed : 12.89 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.45 (0.28), residues: 998 helix: 2.91 (0.22), residues: 576 sheet: 1.42 (0.66), residues: 66 loop : -0.59 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 138 TYR 0.008 0.001 TYR C 114 PHE 0.012 0.001 PHE C 57 TRP 0.022 0.001 TRP C 73 HIS 0.002 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7862) covalent geometry : angle 0.52110 / 0.26 (10704) hydrogen bonds : bond 0.04142 / 2.78 ( 458) hydrogen bonds : angle 3.84635 / 2.73 ( 1362) metal coordination : bond 0.00493 / 0.22 ( 16) metal coordination : angle 0.54640 / 0.29 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.241 Fit side-chains REVERT: B 256 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: C 77 ARG cc_start: 0.6962 (mmp80) cc_final: 0.6668 (mmp80) REVERT: C 110 ASP cc_start: 0.8612 (t0) cc_final: 0.8410 (t0) REVERT: C 256 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7457 (mpp) REVERT: D 1 MET cc_start: 0.7727 (tmm) cc_final: 0.6826 (pmm) REVERT: D 62 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7519 (tmtm) REVERT: D 75 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8586 (mtmm) REVERT: D 137 ASN cc_start: 0.8293 (t0) cc_final: 0.7879 (t0) REVERT: E 1 MET cc_start: 0.7548 (tmm) cc_final: 0.6934 (pmm) REVERT: E 17 ARG cc_start: 0.8779 (ptp-110) cc_final: 0.8576 (ptp-110) REVERT: E 62 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8037 (mttt) REVERT: E 137 ASN cc_start: 0.8371 (t0) cc_final: 0.7987 (t0) outliers start: 14 outliers final: 5 residues processed: 136 average time/residue: 0.7343 time to fit residues: 104.1092 Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.079871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.058883 restraints weight = 12705.960| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.65 r_work: 0.2486 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7878 Z= 0.154 Angle : 0.547 6.996 10712 Z= 0.274 Chirality : 0.040 0.154 1322 Planarity : 0.005 0.043 1318 Dihedral : 5.483 60.285 1136 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.91 % Allowed : 13.37 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.28), residues: 998 helix: 2.93 (0.22), residues: 574 sheet: 1.42 (0.67), residues: 66 loop : -0.68 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 138 TYR 0.011 0.001 TYR C 114 PHE 0.011 0.001 PHE C 57 TRP 0.023 0.002 TRP C 73 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 ( 7862) covalent geometry : angle 0.54709 / 0.27 (10704) hydrogen bonds : bond 0.04808 / 3.24 ( 458) hydrogen bonds : angle 3.99121 / 2.84 ( 1362) metal coordination : bond 0.00753 / 0.31 ( 16) metal coordination : angle 0.88899 / 0.47 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.309 Fit side-chains REVERT: B 205 ARG cc_start: 0.9078 (ttm170) cc_final: 0.8856 (ttm170) REVERT: B 256 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7744 (mpp) REVERT: C 77 ARG cc_start: 0.6900 (mmp80) cc_final: 0.6562 (mmp80) REVERT: C 110 ASP cc_start: 0.8717 (t0) cc_final: 0.8513 (t0) REVERT: C 256 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7655 (mpp) REVERT: D 62 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7538 (tmtm) REVERT: D 75 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8595 (mtmm) REVERT: D 137 ASN cc_start: 0.8498 (t0) cc_final: 0.8039 (t0) REVERT: E 62 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8084 (mttt) REVERT: E 137 ASN cc_start: 0.8482 (t0) cc_final: 0.8028 (t0) outliers start: 16 outliers final: 7 residues processed: 137 average time/residue: 0.7315 time to fit residues: 104.6603 Evaluate side-chains 134 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 153 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.061673 restraints weight = 12440.311| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.63 r_work: 0.2544 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7878 Z= 0.104 Angle : 0.533 10.273 10712 Z= 0.263 Chirality : 0.039 0.150 1322 Planarity : 0.004 0.044 1318 Dihedral : 5.192 54.497 1136 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.67 % Allowed : 14.68 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.54 (0.28), residues: 998 helix: 3.03 (0.22), residues: 574 sheet: 1.43 (0.67), residues: 66 loop : -0.61 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 138 TYR 0.007 0.001 TYR C 114 PHE 0.011 0.001 PHE C 57 TRP 0.022 0.001 TRP C 73 HIS 0.001 0.000 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7862) covalent geometry : angle 0.53326 / 0.26 (10704) hydrogen bonds : bond 0.03718 / 2.50 ( 458) hydrogen bonds : angle 3.78323 / 2.68 ( 1362) metal coordination : bond 0.00354 / 0.20 ( 16) metal coordination : angle 0.29038 / 0.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.301 Fit side-chains REVERT: B 169 LYS cc_start: 0.8349 (mtpp) cc_final: 0.8107 (ttmm) REVERT: B 205 ARG cc_start: 0.9055 (ttm170) cc_final: 0.8829 (ttm-80) REVERT: B 256 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7605 (mpp) REVERT: C 77 ARG cc_start: 0.6996 (mmp80) cc_final: 0.6652 (mmp80) REVERT: C 110 ASP cc_start: 0.8615 (t0) cc_final: 0.8360 (t0) REVERT: C 256 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: D 62 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7473 (tmtm) REVERT: D 137 ASN cc_start: 0.8317 (t0) cc_final: 0.7883 (t0) REVERT: E 1 MET cc_start: 0.7663 (tmm) cc_final: 0.6724 (pmm) REVERT: E 62 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7408 (tmtm) REVERT: E 137 ASN cc_start: 0.8355 (t0) cc_final: 0.7917 (t0) outliers start: 14 outliers final: 5 residues processed: 137 average time/residue: 0.7189 time to fit residues: 103.0449 Evaluate side-chains 132 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 237 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.078727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.057685 restraints weight = 12734.784| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 2.65 r_work: 0.2461 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2327 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7878 Z= 0.199 Angle : 0.606 9.601 10712 Z= 0.300 Chirality : 0.041 0.154 1322 Planarity : 0.005 0.062 1318 Dihedral : 5.553 60.413 1136 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.55 % Allowed : 15.51 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.38 (0.28), residues: 998 helix: 2.94 (0.22), residues: 574 sheet: 1.39 (0.67), residues: 66 loop : -0.75 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 138 TYR 0.013 0.001 TYR C 114 PHE 0.015 0.001 PHE C 116 TRP 0.029 0.002 TRP C 73 HIS 0.003 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 ( 7862) covalent geometry : angle 0.60515 / 0.30 (10704) hydrogen bonds : bond 0.05238 / 3.53 ( 458) hydrogen bonds : angle 4.07133 / 2.90 ( 1362) metal coordination : bond 0.00982 / 0.37 ( 16) metal coordination : angle 1.17355 / 0.64 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.302 Fit side-chains REVERT: B 169 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8338 (ttmm) REVERT: B 256 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7624 (mpp) REVERT: C 110 ASP cc_start: 0.8709 (t0) cc_final: 0.8451 (t0) REVERT: C 256 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7672 (mpp) REVERT: D 62 LYS cc_start: 0.8513 (mtmm) cc_final: 0.7486 (tmtm) REVERT: D 75 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8676 (ptpp) REVERT: D 137 ASN cc_start: 0.8546 (t0) cc_final: 0.8059 (t0) REVERT: E 62 LYS cc_start: 0.8399 (mtpp) cc_final: 0.7391 (tmtm) REVERT: E 137 ASN cc_start: 0.8557 (t0) cc_final: 0.8085 (t0) outliers start: 13 outliers final: 8 residues processed: 137 average time/residue: 0.7775 time to fit residues: 111.0520 Evaluate side-chains 137 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 237 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.058910 restraints weight = 12667.598| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.65 r_work: 0.2488 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7878 Z= 0.148 Angle : 0.596 11.064 10712 Z= 0.294 Chirality : 0.040 0.158 1322 Planarity : 0.005 0.060 1318 Dihedral : 5.515 59.722 1136 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.79 % Allowed : 15.63 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.39 (0.27), residues: 998 helix: 2.96 (0.22), residues: 574 sheet: 1.36 (0.67), residues: 66 loop : -0.75 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 138 TYR 0.010 0.001 TYR C 114 PHE 0.012 0.001 PHE C 116 TRP 0.025 0.002 TRP C 73 HIS 0.002 0.001 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 7862) covalent geometry : angle 0.59556 / 0.29 (10704) hydrogen bonds : bond 0.04600 / 3.11 ( 458) hydrogen bonds : angle 3.98109 / 2.83 ( 1362) metal coordination : bond 0.00642 / 0.28 ( 16) metal coordination : angle 0.71553 / 0.39 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.307 Fit side-chains REVERT: B 256 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7675 (mpp) REVERT: C 110 ASP cc_start: 0.8708 (t0) cc_final: 0.8440 (t0) REVERT: C 166 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8272 (pm20) REVERT: C 256 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7661 (mpp) REVERT: D 62 LYS cc_start: 0.8509 (mtmm) cc_final: 0.7501 (tmtm) REVERT: D 75 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8700 (ptpp) REVERT: D 137 ASN cc_start: 0.8535 (t0) cc_final: 0.8037 (t0) REVERT: E 1 MET cc_start: 0.8055 (tmm) cc_final: 0.6301 (pmm) REVERT: E 28 LYS cc_start: 0.8796 (mppt) cc_final: 0.8574 (mppt) REVERT: E 62 LYS cc_start: 0.8404 (mtpp) cc_final: 0.7400 (tmtm) REVERT: E 137 ASN cc_start: 0.8531 (t0) cc_final: 0.8051 (t0) outliers start: 15 outliers final: 8 residues processed: 134 average time/residue: 0.7782 time to fit residues: 108.7519 Evaluate side-chains 134 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.059752 restraints weight = 12576.760| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.64 r_work: 0.2505 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7878 Z= 0.130 Angle : 0.579 10.428 10712 Z= 0.287 Chirality : 0.039 0.151 1322 Planarity : 0.005 0.062 1318 Dihedral : 5.429 58.936 1136 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.31 % Allowed : 16.35 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.28), residues: 998 helix: 3.00 (0.22), residues: 574 sheet: 1.39 (0.67), residues: 66 loop : -0.76 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 138 TYR 0.009 0.001 TYR C 114 PHE 0.011 0.001 PHE C 57 TRP 0.035 0.002 TRP C 73 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7862) covalent geometry : angle 0.57922 / 0.29 (10704) hydrogen bonds : bond 0.04198 / 2.83 ( 458) hydrogen bonds : angle 3.90035 / 2.77 ( 1362) metal coordination : bond 0.00503 / 0.22 ( 16) metal coordination : angle 0.55324 / 0.31 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.305 Fit side-chains REVERT: B 205 ARG cc_start: 0.8961 (ttm170) cc_final: 0.8740 (ttm-80) REVERT: B 256 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7660 (mpp) REVERT: C 110 ASP cc_start: 0.8707 (t0) cc_final: 0.8470 (t0) REVERT: C 166 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8338 (pm20) REVERT: C 256 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: D 62 LYS cc_start: 0.8488 (mtmm) cc_final: 0.7509 (tmtm) REVERT: D 75 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8763 (ptpp) REVERT: D 137 ASN cc_start: 0.8493 (t0) cc_final: 0.8040 (t0) REVERT: E 1 MET cc_start: 0.8058 (tmm) cc_final: 0.6256 (pmm) REVERT: E 62 LYS cc_start: 0.8399 (mtpp) cc_final: 0.7401 (tmtm) REVERT: E 137 ASN cc_start: 0.8509 (t0) cc_final: 0.8030 (t0) outliers start: 11 outliers final: 8 residues processed: 135 average time/residue: 0.7831 time to fit residues: 110.2682 Evaluate side-chains 135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 256 MET Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 237 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 239 GLN E 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.059429 restraints weight = 11992.880| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.63 r_work: 0.2498 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7878 Z= 0.142 Angle : 0.605 10.236 10712 Z= 0.300 Chirality : 0.040 0.154 1322 Planarity : 0.005 0.064 1318 Dihedral : 5.468 59.826 1136 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.19 % Allowed : 16.59 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.42 (0.28), residues: 998 helix: 3.00 (0.22), residues: 574 sheet: 1.42 (0.67), residues: 66 loop : -0.79 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 138 TYR 0.011 0.001 TYR C 114 PHE 0.011 0.001 PHE C 57 TRP 0.033 0.002 TRP C 73 HIS 0.002 0.000 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 7862) covalent geometry : angle 0.60441 / 0.30 (10704) hydrogen bonds : bond 0.04395 / 2.97 ( 458) hydrogen bonds : angle 3.93595 / 2.79 ( 1362) metal coordination : bond 0.00600 / 0.25 ( 16) metal coordination : angle 0.75112 / 0.42 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3042.60 seconds wall clock time: 52 minutes 26.59 seconds (3146.59 seconds total)