Starting phenix.real_space_refine on Mon Jul 28 13:54:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbo_16547/07_2025/8cbo_16547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbo_16547/07_2025/8cbo_16547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2025/8cbo_16547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2025/8cbo_16547.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2025/8cbo_16547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbo_16547/07_2025/8cbo_16547.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 44 5.16 5 C 6431 2.51 5 N 1856 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10574 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1747 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "T" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1233 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 23, 'rna3p_pyr': 22} Link IDs: {'rna2p': 13, 'rna3p': 44} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 8.45, per 1000 atoms: 0.80 Number of scatterers: 10574 At special positions: 0 Unit cell: (95.436, 87.483, 133.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 66 15.00 O 2177 8.00 N 1856 7.00 C 6431 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: 3.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 51.5% alpha, 10.4% beta 14 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.180A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 138 removed outlier: 3.529A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 165 through 186 removed outlier: 4.457A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.122A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.573A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.126A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 139 removed outlier: 3.797A pdb=" N MET B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 186 removed outlier: 4.583A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 4.067A pdb=" N SER B 208 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.524A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.867A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.661A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 186 removed outlier: 4.576A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.642A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.622A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 138 removed outlier: 3.570A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 187 removed outlier: 4.511A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.556A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 182 through 202 removed outlier: 3.707A pdb=" N GLN E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 236 Processing helix chain 'E' and resid 252 through 263 Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.976A pdb=" N ASP E 267 " --> pdb=" O GLU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.577A pdb=" N TYR E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 364 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 374 through 376 No H-bonds generated for 'chain 'E' and resid 374 through 376' Processing helix chain 'E' and resid 377 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.837A pdb=" N ALA A 13 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU A 40 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 15 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.290A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 13 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 40 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 15 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.315A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 196 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ILE C 251 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 195 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.435A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA D 13 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU D 40 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 15 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL D 12 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL D 89 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 14 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 272 through 274 removed outlier: 6.313A pdb=" N LEU E 205 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N CYS E 246 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE E 207 " --> pdb=" O CYS E 246 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ILE E 309 " --> pdb=" O PRO E 204 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 206 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE E 288 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 332 " --> pdb=" O ILE E 287 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2285 1.33 - 1.45: 2455 1.45 - 1.57: 5939 1.57 - 1.69: 129 1.69 - 1.81: 73 Bond restraints: 10881 Sorted by residual: bond pdb=" C GLY E 320 " pdb=" N THR E 321 " ideal model delta sigma weight residual 1.332 1.418 -0.086 1.40e-02 5.10e+03 3.78e+01 bond pdb=" C GLY B 202 " pdb=" N THR B 203 " ideal model delta sigma weight residual 1.327 1.272 0.054 1.19e-02 7.06e+03 2.09e+01 bond pdb=" CA SER E 322 " pdb=" CB SER E 322 " ideal model delta sigma weight residual 1.529 1.458 0.072 1.58e-02 4.01e+03 2.06e+01 bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.580 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14593 1.47 - 2.94: 314 2.94 - 4.41: 115 4.41 - 5.89: 24 5.89 - 7.36: 6 Bond angle restraints: 15052 Sorted by residual: angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" N PRO B 204 " ideal model delta sigma weight residual 117.68 122.78 -5.10 7.10e-01 1.98e+00 5.15e+01 angle pdb=" C GLN E 221 " pdb=" N ASN E 222 " pdb=" CA ASN E 222 " ideal model delta sigma weight residual 120.44 113.47 6.97 1.30e+00 5.92e-01 2.88e+01 angle pdb=" C TYR E 211 " pdb=" CA TYR E 211 " pdb=" CB TYR E 211 " ideal model delta sigma weight residual 111.06 103.70 7.36 1.55e+00 4.16e-01 2.25e+01 angle pdb=" CA THR B 203 " pdb=" C THR B 203 " pdb=" O THR B 203 " ideal model delta sigma weight residual 120.71 116.77 3.94 8.70e-01 1.32e+00 2.05e+01 angle pdb=" CA GLY E 320 " pdb=" C GLY E 320 " pdb=" N THR E 321 " ideal model delta sigma weight residual 118.42 112.91 5.51 1.26e+00 6.30e-01 1.91e+01 ... (remaining 15047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 6376 33.53 - 67.05: 281 67.05 - 100.58: 27 100.58 - 134.11: 0 134.11 - 167.63: 1 Dihedral angle restraints: 6685 sinusoidal: 3244 harmonic: 3441 Sorted by residual: dihedral pdb=" O4' A T 14 " pdb=" C1' A T 14 " pdb=" N9 A T 14 " pdb=" C4 A T 14 " ideal model delta sinusoidal sigma weight residual -78.00 -16.71 -61.29 1 1.70e+01 3.46e-03 1.73e+01 dihedral pdb=" O4' G T 30 " pdb=" C1' G T 30 " pdb=" N9 G T 30 " pdb=" C4 G T 30 " ideal model delta sinusoidal sigma weight residual -106.00 -164.50 58.50 1 1.70e+01 3.46e-03 1.59e+01 dihedral pdb=" C4' A T 7 " pdb=" C3' A T 7 " pdb=" O3' A T 7 " pdb=" P U T 8 " ideal model delta sinusoidal sigma weight residual -140.00 27.63 -167.63 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 6682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1553 0.054 - 0.107: 171 0.107 - 0.161: 65 0.161 - 0.215: 3 0.215 - 0.268: 1 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA TYR E 211 " pdb=" N TYR E 211 " pdb=" C TYR E 211 " pdb=" CB TYR E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2' SAH E 401 " pdb=" C1' SAH E 401 " pdb=" C3' SAH E 401 " pdb=" O2' SAH E 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1D NAD C 301 " pdb=" C2D NAD C 301 " pdb=" N1N NAD C 301 " pdb=" O4D NAD C 301 " both_signs ideal model delta sigma weight residual False 2.41 2.59 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1790 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.044 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 320 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C GLY E 320 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY E 320 " 0.025 2.00e-02 2.50e+03 pdb=" N THR E 321 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.027 2.00e-02 2.50e+03 1.56e-02 4.87e+00 pdb=" C2N NAD B 301 " 0.009 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " -0.012 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " -0.011 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.024 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1281 2.74 - 3.28: 10605 3.28 - 3.82: 18984 3.82 - 4.36: 23797 4.36 - 4.90: 39164 Nonbonded interactions: 93831 Sorted by model distance: nonbonded pdb=" OG1 THR C 153 " pdb=" OH TYR C 233 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG C 184 " pdb=" O GLY D 161 " model vdw 2.212 3.120 nonbonded pdb=" OG1 THR A 179 " pdb=" OG1 THR A 195 " model vdw 2.212 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG SER D 219 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR E 211 " pdb=" OH TYR E 289 " model vdw 2.260 3.040 ... (remaining 93826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 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: 80.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.790 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.005 0.086 10881 Z= 0.239 Angle : 0.607 7.357 15052 Z= 0.316 Chirality : 0.041 0.268 1793 Planarity : 0.004 0.038 1729 Dihedral : 17.263 167.633 4489 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.21 % Allowed : 0.73 % Favored : 99.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1221 helix: 1.89 (0.23), residues: 550 sheet: -1.26 (0.37), residues: 201 loop : -0.54 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 193 HIS 0.002 0.001 HIS A 109 PHE 0.017 0.001 PHE D 245 TYR 0.019 0.002 TYR E 289 ARG 0.002 0.000 ARG B 147 Details of bonding type rmsd hydrogen bonds : bond 0.12938 ( 479) hydrogen bonds : angle 6.17393 ( 1337) covalent geometry : bond 0.00459 (10881) covalent geometry : angle 0.60722 (15052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 317 MET cc_start: 0.7399 (mmm) cc_final: 0.6927 (mmt) REVERT: E 344 TRP cc_start: 0.6673 (t-100) cc_final: 0.6317 (t-100) REVERT: E 354 ASP cc_start: 0.7278 (p0) cc_final: 0.6762 (p0) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.3205 time to fit residues: 104.8118 Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 321 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN E 203 GLN E 222 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN ** E 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.092717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064767 restraints weight = 28940.111| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.99 r_work: 0.3026 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10881 Z= 0.146 Angle : 0.558 6.350 15052 Z= 0.283 Chirality : 0.041 0.177 1793 Planarity : 0.004 0.043 1729 Dihedral : 16.408 162.066 2384 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.83 % Allowed : 9.91 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1221 helix: 2.40 (0.23), residues: 550 sheet: -1.15 (0.41), residues: 171 loop : -0.29 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 183 HIS 0.003 0.001 HIS E 303 PHE 0.013 0.001 PHE D 126 TYR 0.013 0.001 TYR A 168 ARG 0.005 0.001 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 479) hydrogen bonds : angle 5.03916 ( 1337) covalent geometry : bond 0.00331 (10881) covalent geometry : angle 0.55842 (15052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 70 ASP cc_start: 0.9135 (m-30) cc_final: 0.8731 (m-30) REVERT: A 249 GLU cc_start: 0.8437 (tp30) cc_final: 0.8031 (tp30) REVERT: B 86 ASP cc_start: 0.8600 (t0) cc_final: 0.8399 (m-30) REVERT: B 99 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9073 (mptt) REVERT: B 203 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 119 ASP cc_start: 0.9121 (m-30) cc_final: 0.8911 (m-30) REVERT: C 147 ARG cc_start: 0.8809 (mtt90) cc_final: 0.8244 (ttm-80) REVERT: C 249 GLU cc_start: 0.8407 (tp30) cc_final: 0.7374 (tp30) REVERT: D 81 LYS cc_start: 0.9603 (tppt) cc_final: 0.9361 (tppt) REVERT: D 254 ASP cc_start: 0.8809 (p0) cc_final: 0.8491 (p0) REVERT: E 344 TRP cc_start: 0.6708 (t-100) cc_final: 0.6490 (t-100) outliers start: 8 outliers final: 5 residues processed: 191 average time/residue: 0.3691 time to fit residues: 95.5212 Evaluate side-chains 142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.0010 chunk 121 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.089293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064101 restraints weight = 28305.409| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.84 r_work: 0.2995 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10881 Z= 0.173 Angle : 0.549 7.400 15052 Z= 0.277 Chirality : 0.040 0.141 1793 Planarity : 0.004 0.039 1729 Dihedral : 16.185 159.521 2383 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.36 % Allowed : 11.57 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1221 helix: 2.65 (0.23), residues: 549 sheet: -0.63 (0.46), residues: 143 loop : -0.40 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 183 HIS 0.003 0.001 HIS E 303 PHE 0.015 0.002 PHE B 82 TYR 0.009 0.001 TYR E 244 ARG 0.007 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 479) hydrogen bonds : angle 4.96766 ( 1337) covalent geometry : bond 0.00389 (10881) covalent geometry : angle 0.54860 (15052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9109 (m-30) cc_final: 0.8814 (m-30) REVERT: A 104 LYS cc_start: 0.9253 (mmtm) cc_final: 0.8700 (mmtm) REVERT: A 160 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: A 249 GLU cc_start: 0.8571 (tp30) cc_final: 0.8357 (tp30) REVERT: B 99 LYS cc_start: 0.9599 (mtpt) cc_final: 0.9100 (mptt) REVERT: B 203 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 81 LYS cc_start: 0.9429 (tppp) cc_final: 0.9053 (tppp) REVERT: C 119 ASP cc_start: 0.9165 (m-30) cc_final: 0.8903 (m-30) REVERT: C 147 ARG cc_start: 0.8795 (mtt90) cc_final: 0.8571 (mtt90) REVERT: D 81 LYS cc_start: 0.9601 (tppt) cc_final: 0.9346 (tppt) REVERT: D 242 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8676 (mm-30) REVERT: E 187 MET cc_start: 0.9193 (mtp) cc_final: 0.8881 (mtt) REVERT: E 231 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8432 (tm-30) REVERT: E 298 MET cc_start: 0.8954 (ttt) cc_final: 0.8652 (ttt) REVERT: E 344 TRP cc_start: 0.6764 (t-100) cc_final: 0.6535 (t-100) outliers start: 13 outliers final: 4 residues processed: 176 average time/residue: 0.3728 time to fit residues: 86.8356 Evaluate side-chains 145 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065478 restraints weight = 27915.479| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.80 r_work: 0.3055 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10881 Z= 0.113 Angle : 0.529 7.804 15052 Z= 0.265 Chirality : 0.039 0.135 1793 Planarity : 0.004 0.042 1729 Dihedral : 15.939 158.750 2383 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.04 % Allowed : 13.35 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1221 helix: 2.71 (0.23), residues: 548 sheet: -0.81 (0.38), residues: 185 loop : -0.22 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 PHE 0.016 0.001 PHE E 179 TYR 0.008 0.001 TYR E 244 ARG 0.008 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 479) hydrogen bonds : angle 4.72403 ( 1337) covalent geometry : bond 0.00262 (10881) covalent geometry : angle 0.52855 (15052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8680 (mt-10) REVERT: A 70 ASP cc_start: 0.9121 (m-30) cc_final: 0.8857 (m-30) REVERT: A 104 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8637 (mmtm) REVERT: A 160 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: A 185 ASP cc_start: 0.8541 (m-30) cc_final: 0.8225 (m-30) REVERT: B 99 LYS cc_start: 0.9607 (mtpt) cc_final: 0.9118 (mptt) REVERT: B 203 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8834 (p) REVERT: C 28 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8465 (mt-10) REVERT: C 81 LYS cc_start: 0.9471 (tppp) cc_final: 0.9117 (tppp) REVERT: C 119 ASP cc_start: 0.9106 (m-30) cc_final: 0.8894 (m-30) REVERT: D 70 ASP cc_start: 0.9105 (m-30) cc_final: 0.8745 (t0) REVERT: D 242 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8680 (mm-30) REVERT: E 219 GLU cc_start: 0.9001 (mp0) cc_final: 0.8354 (pt0) outliers start: 10 outliers final: 4 residues processed: 180 average time/residue: 0.2759 time to fit residues: 67.3657 Evaluate side-chains 142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 50 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.090310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064374 restraints weight = 28107.152| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.82 r_work: 0.3031 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10881 Z= 0.132 Angle : 0.534 7.824 15052 Z= 0.266 Chirality : 0.039 0.129 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.901 159.207 2383 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.04 % Allowed : 13.45 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1221 helix: 2.77 (0.23), residues: 548 sheet: -0.79 (0.38), residues: 185 loop : -0.15 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 183 HIS 0.002 0.001 HIS E 242 PHE 0.019 0.001 PHE E 179 TYR 0.019 0.001 TYR A 168 ARG 0.009 0.001 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 479) hydrogen bonds : angle 4.66849 ( 1337) covalent geometry : bond 0.00307 (10881) covalent geometry : angle 0.53387 (15052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9126 (m-30) cc_final: 0.8798 (m-30) REVERT: A 104 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8613 (mmtm) REVERT: A 142 ASP cc_start: 0.8823 (t0) cc_final: 0.8604 (t0) REVERT: A 160 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: A 185 ASP cc_start: 0.8521 (m-30) cc_final: 0.8232 (m-30) REVERT: A 249 GLU cc_start: 0.8793 (tp30) cc_final: 0.8319 (tp30) REVERT: B 99 LYS cc_start: 0.9617 (mtpt) cc_final: 0.9119 (mptt) REVERT: B 203 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8852 (p) REVERT: C 28 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8489 (mt-10) REVERT: D 70 ASP cc_start: 0.9088 (m-30) cc_final: 0.8740 (t0) REVERT: D 242 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8673 (mm-30) outliers start: 10 outliers final: 7 residues processed: 167 average time/residue: 0.3020 time to fit residues: 68.2359 Evaluate side-chains 138 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.090537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065973 restraints weight = 27986.229| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.77 r_work: 0.3087 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10881 Z= 0.110 Angle : 0.536 7.607 15052 Z= 0.267 Chirality : 0.039 0.134 1793 Planarity : 0.004 0.041 1729 Dihedral : 15.801 159.041 2383 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.25 % Allowed : 13.97 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1221 helix: 2.72 (0.22), residues: 548 sheet: -0.69 (0.39), residues: 183 loop : -0.07 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 233 HIS 0.001 0.000 HIS E 242 PHE 0.019 0.001 PHE E 179 TYR 0.007 0.001 TYR D 168 ARG 0.008 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 479) hydrogen bonds : angle 4.54271 ( 1337) covalent geometry : bond 0.00256 (10881) covalent geometry : angle 0.53582 (15052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9126 (m-30) cc_final: 0.8838 (m-30) REVERT: A 104 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8598 (mmtm) REVERT: A 160 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: A 185 ASP cc_start: 0.8509 (m-30) cc_final: 0.8279 (m-30) REVERT: B 99 LYS cc_start: 0.9609 (mtpt) cc_final: 0.9113 (mptt) REVERT: B 105 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9216 (mttp) REVERT: B 203 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8826 (p) REVERT: C 28 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8517 (mt-10) REVERT: C 119 ASP cc_start: 0.9068 (m-30) cc_final: 0.8857 (m-30) REVERT: C 140 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 211 GLU cc_start: 0.8461 (mp0) cc_final: 0.8241 (mp0) REVERT: D 70 ASP cc_start: 0.9064 (m-30) cc_final: 0.8701 (t0) REVERT: D 242 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8671 (mm-30) REVERT: E 219 GLU cc_start: 0.9030 (mp0) cc_final: 0.8264 (pt0) REVERT: E 384 PHE cc_start: 0.7616 (m-80) cc_final: 0.6852 (m-80) outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 0.2790 time to fit residues: 59.8351 Evaluate side-chains 136 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.091299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064478 restraints weight = 29555.956| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.98 r_work: 0.3060 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10881 Z= 0.127 Angle : 0.556 7.627 15052 Z= 0.277 Chirality : 0.039 0.132 1793 Planarity : 0.004 0.050 1729 Dihedral : 15.733 159.274 2383 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.94 % Allowed : 14.70 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1221 helix: 2.76 (0.23), residues: 549 sheet: -0.68 (0.39), residues: 183 loop : -0.13 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 183 HIS 0.002 0.000 HIS E 242 PHE 0.017 0.001 PHE E 179 TYR 0.015 0.001 TYR A 168 ARG 0.010 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 479) hydrogen bonds : angle 4.51474 ( 1337) covalent geometry : bond 0.00297 (10881) covalent geometry : angle 0.55563 (15052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.9132 (m-30) cc_final: 0.8840 (m-30) REVERT: A 104 LYS cc_start: 0.9221 (mmtm) cc_final: 0.8640 (mmtm) REVERT: A 160 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: A 185 ASP cc_start: 0.8534 (m-30) cc_final: 0.8309 (m-30) REVERT: B 99 LYS cc_start: 0.9624 (mtpt) cc_final: 0.9090 (mptt) REVERT: B 105 LYS cc_start: 0.9488 (mtmt) cc_final: 0.9240 (mttp) REVERT: B 203 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8843 (p) REVERT: C 28 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8551 (mt-10) REVERT: C 119 ASP cc_start: 0.9105 (m-30) cc_final: 0.8838 (m-30) REVERT: C 140 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8464 (tm-30) REVERT: C 147 ARG cc_start: 0.8821 (mtt90) cc_final: 0.8490 (ttm-80) REVERT: C 211 GLU cc_start: 0.8465 (mp0) cc_final: 0.8252 (mp0) REVERT: D 70 ASP cc_start: 0.9091 (m-30) cc_final: 0.8726 (t0) REVERT: D 242 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8702 (mm-30) REVERT: E 215 MET cc_start: 0.8146 (mtm) cc_final: 0.7695 (mtm) REVERT: E 219 GLU cc_start: 0.9027 (mp0) cc_final: 0.8372 (pt0) REVERT: E 344 TRP cc_start: 0.7007 (t-100) cc_final: 0.6516 (t-100) REVERT: E 384 PHE cc_start: 0.7635 (m-80) cc_final: 0.6930 (m-80) outliers start: 9 outliers final: 7 residues processed: 159 average time/residue: 0.2596 time to fit residues: 56.1749 Evaluate side-chains 142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063080 restraints weight = 28344.392| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.81 r_work: 0.3033 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10881 Z= 0.171 Angle : 0.587 7.863 15052 Z= 0.293 Chirality : 0.039 0.136 1793 Planarity : 0.004 0.046 1729 Dihedral : 15.784 159.344 2383 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.25 % Allowed : 14.39 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1221 helix: 2.71 (0.23), residues: 549 sheet: -0.71 (0.38), residues: 183 loop : -0.20 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 183 HIS 0.002 0.001 HIS E 242 PHE 0.018 0.001 PHE E 179 TYR 0.007 0.001 TYR E 214 ARG 0.010 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 479) hydrogen bonds : angle 4.64354 ( 1337) covalent geometry : bond 0.00395 (10881) covalent geometry : angle 0.58695 (15052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8775 (mt-10) REVERT: A 70 ASP cc_start: 0.9106 (m-30) cc_final: 0.8802 (m-30) REVERT: A 104 LYS cc_start: 0.9264 (mmtm) cc_final: 0.8716 (mmtm) REVERT: A 185 ASP cc_start: 0.8509 (m-30) cc_final: 0.8272 (m-30) REVERT: A 249 GLU cc_start: 0.8417 (tp30) cc_final: 0.7914 (tp30) REVERT: C 28 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8442 (mt-10) REVERT: C 119 ASP cc_start: 0.9133 (m-30) cc_final: 0.8902 (m-30) REVERT: C 140 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 147 ARG cc_start: 0.8873 (mtt90) cc_final: 0.8591 (ttm-80) REVERT: C 211 GLU cc_start: 0.8479 (mp0) cc_final: 0.8259 (mp0) REVERT: D 70 ASP cc_start: 0.9087 (m-30) cc_final: 0.8738 (t0) REVERT: D 242 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8664 (mm-30) REVERT: E 384 PHE cc_start: 0.7694 (m-80) cc_final: 0.6953 (m-80) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.2408 time to fit residues: 49.9984 Evaluate side-chains 142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.088412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062798 restraints weight = 28566.357| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.82 r_work: 0.3022 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10881 Z= 0.175 Angle : 0.608 8.304 15052 Z= 0.303 Chirality : 0.040 0.145 1793 Planarity : 0.004 0.040 1729 Dihedral : 15.770 159.127 2383 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.94 % Allowed : 15.85 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1221 helix: 2.66 (0.23), residues: 549 sheet: -0.71 (0.39), residues: 183 loop : -0.21 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 183 HIS 0.002 0.001 HIS E 242 PHE 0.017 0.001 PHE E 179 TYR 0.020 0.001 TYR A 168 ARG 0.007 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 479) hydrogen bonds : angle 4.64058 ( 1337) covalent geometry : bond 0.00405 (10881) covalent geometry : angle 0.60827 (15052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 70 ASP cc_start: 0.9107 (m-30) cc_final: 0.8801 (m-30) REVERT: A 104 LYS cc_start: 0.9268 (mmtm) cc_final: 0.8728 (mmtm) REVERT: A 147 ARG cc_start: 0.9283 (mtt90) cc_final: 0.9000 (ttm-80) REVERT: A 185 ASP cc_start: 0.8507 (m-30) cc_final: 0.8259 (m-30) REVERT: A 249 GLU cc_start: 0.8403 (tp30) cc_final: 0.7920 (tp30) REVERT: C 28 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8547 (mt-10) REVERT: C 119 ASP cc_start: 0.9153 (m-30) cc_final: 0.8929 (m-30) REVERT: C 147 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8488 (ttm-80) REVERT: C 211 GLU cc_start: 0.8471 (mp0) cc_final: 0.8246 (mp0) REVERT: D 70 ASP cc_start: 0.9102 (m-30) cc_final: 0.8770 (t0) REVERT: D 242 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8675 (mm-30) REVERT: E 298 MET cc_start: 0.9060 (ttt) cc_final: 0.8723 (ttt) REVERT: E 334 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7826 (mt-10) REVERT: E 384 PHE cc_start: 0.7702 (m-80) cc_final: 0.6981 (m-80) outliers start: 9 outliers final: 9 residues processed: 147 average time/residue: 0.2428 time to fit residues: 49.9500 Evaluate side-chains 145 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.090160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.063367 restraints weight = 29530.441| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.98 r_work: 0.3040 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10881 Z= 0.143 Angle : 0.613 8.716 15052 Z= 0.307 Chirality : 0.040 0.167 1793 Planarity : 0.004 0.045 1729 Dihedral : 15.688 158.882 2383 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.94 % Allowed : 15.95 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1221 helix: 2.59 (0.23), residues: 549 sheet: -0.67 (0.39), residues: 183 loop : -0.15 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 233 HIS 0.002 0.001 HIS E 242 PHE 0.016 0.001 PHE E 179 TYR 0.006 0.001 TYR D 168 ARG 0.007 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 479) hydrogen bonds : angle 4.60890 ( 1337) covalent geometry : bond 0.00337 (10881) covalent geometry : angle 0.61273 (15052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 40 LEU cc_start: 0.9645 (tt) cc_final: 0.9436 (tt) REVERT: A 70 ASP cc_start: 0.9092 (m-30) cc_final: 0.8799 (m-30) REVERT: A 104 LYS cc_start: 0.9245 (mmtm) cc_final: 0.8667 (mmtm) REVERT: A 147 ARG cc_start: 0.9288 (mtt90) cc_final: 0.8959 (ttm-80) REVERT: A 185 ASP cc_start: 0.8544 (m-30) cc_final: 0.8308 (m-30) REVERT: A 249 GLU cc_start: 0.8378 (tp30) cc_final: 0.7937 (tp30) REVERT: B 113 ASP cc_start: 0.9028 (m-30) cc_final: 0.8733 (t0) REVERT: B 194 MET cc_start: 0.8937 (tpt) cc_final: 0.8700 (tpt) REVERT: B 203 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 28 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8561 (mt-10) REVERT: C 119 ASP cc_start: 0.9141 (m-30) cc_final: 0.8909 (m-30) REVERT: C 147 ARG cc_start: 0.8841 (mtt90) cc_final: 0.8423 (ttm-80) REVERT: C 211 GLU cc_start: 0.8486 (mp0) cc_final: 0.8277 (pm20) REVERT: D 70 ASP cc_start: 0.9114 (m-30) cc_final: 0.8846 (m-30) REVERT: D 242 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8679 (mm-30) REVERT: E 298 MET cc_start: 0.9067 (ttt) cc_final: 0.8335 (ttt) REVERT: E 334 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7822 (mm-30) REVERT: E 344 TRP cc_start: 0.7051 (t-100) cc_final: 0.6619 (t-100) REVERT: E 384 PHE cc_start: 0.7706 (m-80) cc_final: 0.6996 (m-80) outliers start: 9 outliers final: 6 residues processed: 152 average time/residue: 0.2317 time to fit residues: 49.7560 Evaluate side-chains 145 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 109 optimal weight: 0.0870 chunk 123 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 ASN ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.090124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063312 restraints weight = 29422.561| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.96 r_work: 0.3041 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10881 Z= 0.144 Angle : 0.613 9.055 15052 Z= 0.308 Chirality : 0.040 0.208 1793 Planarity : 0.004 0.043 1729 Dihedral : 15.657 159.036 2383 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.73 % Allowed : 15.95 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1221 helix: 2.59 (0.23), residues: 549 sheet: -0.66 (0.39), residues: 183 loop : -0.16 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 183 HIS 0.002 0.001 HIS E 242 PHE 0.019 0.001 PHE E 179 TYR 0.021 0.001 TYR A 168 ARG 0.006 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 479) hydrogen bonds : angle 4.61404 ( 1337) covalent geometry : bond 0.00341 (10881) covalent geometry : angle 0.61327 (15052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.83 seconds wall clock time: 97 minutes 58.72 seconds (5878.72 seconds total)