Starting phenix.real_space_refine on Wed Mar 4 08:53:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vdk_21151/03_2026/6vdk_21151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vdk_21151/03_2026/6vdk_21151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vdk_21151/03_2026/6vdk_21151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vdk_21151/03_2026/6vdk_21151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vdk_21151/03_2026/6vdk_21151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vdk_21151/03_2026/6vdk_21151.map" } resolution = 4.5 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= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 102 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7498 2.51 5 N 2210 2.21 5 O 2455 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12309 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2129 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2083 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2128 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2067 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "E" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 26} Chain: "F" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'DNA': 27} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 463 Classifications: {'peptide': 56} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 52} Chain: "J" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 456 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "P" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DLU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DLU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.96, per 1000 atoms: 0.24 Number of scatterers: 12309 At special positions: 0 Unit cell: (111.3, 131.44, 103.88, 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) S 36 16.00 P 102 15.00 Mg 4 11.99 F 4 9.00 O 2455 8.00 N 2210 7.00 C 7498 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: 0.90 Conformation dependent library (CDL) restraints added in 385.9 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 40.7% alpha, 21.1% beta 48 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.544A pdb=" N ALA A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.576A pdb=" N LYS A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.511A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.641A pdb=" N LYS A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.928A pdb=" N GLU B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.721A pdb=" N ALA B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.741A pdb=" N THR B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 147 through 166 removed outlier: 3.675A pdb=" N GLU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 186 Processing helix chain 'B' and resid 196 through 221 removed outlier: 4.160A pdb=" N ILE B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 29 through 40 removed outlier: 3.623A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 119 through 122 removed outlier: 3.501A pdb=" N THR C 122 " --> pdb=" O SER C 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 122' Processing helix chain 'C' and resid 123 through 134 removed outlier: 3.853A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 166 Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.513A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 221 removed outlier: 3.742A pdb=" N LEU C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 5 removed outlier: 4.311A pdb=" N ILE D 5 " --> pdb=" O LEU D 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 5' Processing helix chain 'D' and resid 6 through 15 removed outlier: 3.830A pdb=" N GLU D 10 " --> pdb=" O ASP D 6 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 29 through 39 removed outlier: 3.895A pdb=" N ALA D 33 " --> pdb=" O PRO D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 108 removed outlier: 3.657A pdb=" N THR D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.707A pdb=" N THR D 122 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 134 removed outlier: 3.922A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 166 removed outlier: 3.648A pdb=" N GLU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 186 Processing helix chain 'D' and resid 196 through 221 removed outlier: 4.391A pdb=" N ASP D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP D 207 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 275 removed outlier: 3.837A pdb=" N GLN J 274 " --> pdb=" O TYR J 271 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET J 275 " --> pdb=" O GLY J 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 271 through 275' Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.569A pdb=" N LEU A 63 " --> pdb=" O HIS A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 6.975A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL A 225 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 89 removed outlier: 3.709A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP B 61 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 113 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.830A pdb=" N VAL B 250 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 234 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP B 229 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL B 225 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 88 removed outlier: 4.050A pdb=" N LEU C 63 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 257 through 261 removed outlier: 7.156A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL C 225 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 83 through 89 removed outlier: 3.562A pdb=" N VAL D 72 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP D 61 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL D 113 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 225 through 228 removed outlier: 6.679A pdb=" N TYR D 227 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY D 237 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 258 through 261 removed outlier: 7.659A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL I 225 " --> pdb=" O PRO I 238 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG I 224 " --> pdb=" O ILE I 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 257 through 261 removed outlier: 7.380A pdb=" N ALA J 248 " --> pdb=" O LYS J 244 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS J 244 " --> pdb=" O ALA J 248 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL J 250 " --> pdb=" O LEU J 242 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 257 through 261 removed outlier: 6.818A pdb=" N VAL M 250 " --> pdb=" O LEU M 242 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL M 225 " --> pdb=" O PRO M 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 257 through 261 removed outlier: 6.822A pdb=" N VAL P 250 " --> pdb=" O LEU P 242 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL P 225 " --> pdb=" O PRO P 238 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1821 1.31 - 1.43: 3846 1.43 - 1.56: 6855 1.56 - 1.69: 209 1.69 - 1.81: 52 Bond restraints: 12783 Sorted by residual: bond pdb=" CBB DLU C 303 " pdb=" NBC DLU C 303 " ideal model delta sigma weight residual 1.453 1.641 -0.188 2.00e-02 2.50e+03 8.87e+01 bond pdb=" CAW DLU C 303 " pdb=" CAY DLU C 303 " ideal model delta sigma weight residual 1.365 1.553 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" CBB DLU A 303 " pdb=" NBC DLU A 303 " ideal model delta sigma weight residual 1.453 1.640 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" CAW DLU A 303 " pdb=" CAY DLU A 303 " ideal model delta sigma weight residual 1.365 1.552 -0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" CAK DLU C 303 " pdb=" NBD DLU C 303 " ideal model delta sigma weight residual 1.327 1.504 -0.177 2.00e-02 2.50e+03 7.87e+01 ... (remaining 12778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 17248 2.57 - 5.14: 428 5.14 - 7.70: 29 7.70 - 10.27: 6 10.27 - 12.84: 8 Bond angle restraints: 17719 Sorted by residual: angle pdb=" CA PRO P 233 " pdb=" N PRO P 233 " pdb=" CD PRO P 233 " ideal model delta sigma weight residual 112.00 99.16 12.84 1.40e+00 5.10e-01 8.41e+01 angle pdb=" CA PRO M 233 " pdb=" N PRO M 233 " pdb=" CD PRO M 233 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.34e+01 angle pdb=" CA PRO J 233 " pdb=" N PRO J 233 " pdb=" CD PRO J 233 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO I 233 " pdb=" N PRO I 233 " pdb=" CD PRO I 233 " ideal model delta sigma weight residual 112.00 99.36 12.64 1.40e+00 5.10e-01 8.15e+01 angle pdb=" C ASP B 232 " pdb=" N PRO B 233 " pdb=" CA PRO B 233 " ideal model delta sigma weight residual 120.47 124.93 -4.46 1.07e+00 8.73e-01 1.74e+01 ... (remaining 17714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5793 17.76 - 35.52: 912 35.52 - 53.28: 517 53.28 - 71.04: 180 71.04 - 88.81: 29 Dihedral angle restraints: 7431 sinusoidal: 3776 harmonic: 3655 Sorted by residual: dihedral pdb=" CA ILE C 141 " pdb=" C ILE C 141 " pdb=" N PRO C 142 " pdb=" CA PRO C 142 " ideal model delta harmonic sigma weight residual 180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN A 44 " pdb=" C GLN A 44 " pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta harmonic sigma weight residual 180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN B 164 " pdb=" C GLN B 164 " pdb=" N VAL B 165 " pdb=" CA VAL B 165 " ideal model delta harmonic sigma weight residual 180.00 -157.78 -22.22 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1427 0.061 - 0.122: 411 0.122 - 0.183: 83 0.183 - 0.244: 5 0.244 - 0.305: 3 Chirality restraints: 1929 Sorted by residual: chirality pdb=" C1' DC E 38 " pdb=" O4' DC E 38 " pdb=" C2' DC E 38 " pdb=" N1 DC E 38 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE D 257 " pdb=" CA ILE D 257 " pdb=" CG1 ILE D 257 " pdb=" CG2 ILE D 257 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1' DC G 38 " pdb=" O4' DC G 38 " pdb=" C2' DC G 38 " pdb=" N1 DC G 38 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1926 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 232 " 0.059 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO J 233 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO J 233 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 233 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 144 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO C 145 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 145 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 145 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 144 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 145 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.037 5.00e-02 4.00e+02 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 87 2.47 - 3.08: 7387 3.08 - 3.68: 21247 3.68 - 4.29: 29127 4.29 - 4.90: 43993 Nonbonded interactions: 101841 Sorted by model distance: nonbonded pdb="MG MG C 301 " pdb=" OAE DLU C 303 " model vdw 1.860 2.170 nonbonded pdb=" OE1 GLU A 152 " pdb="MG MG A 302 " model vdw 1.961 2.170 nonbonded pdb=" OD2 ASP A 64 " pdb="MG MG A 301 " model vdw 2.074 2.170 nonbonded pdb="MG MG C 302 " pdb=" OAE DLU C 303 " model vdw 2.114 2.170 nonbonded pdb="MG MG A 301 " pdb=" OAE DLU A 303 " model vdw 2.146 2.170 ... (remaining 101836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 48 or resid 56 through 270)) selection = (chain 'B' and (resid 2 through 48 or resid 56 through 270)) selection = (chain 'C' and (resid 2 through 48 or resid 56 through 270)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 222 through 270) selection = (chain 'J' and resid 222 through 270) selection = chain 'M' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 3.430 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.008 0.188 12783 Z= 0.410 Angle : 0.972 12.840 17719 Z= 0.572 Chirality : 0.058 0.305 1929 Planarity : 0.007 0.082 1900 Dihedral : 22.806 88.805 5077 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.46 % Favored : 93.22 % Rotamer: Outliers : 0.65 % Allowed : 8.40 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -3.91 (0.19), residues: 1254 helix: -2.37 (0.18), residues: 457 sheet: -2.53 (0.28), residues: 268 loop : -2.66 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.015 0.002 TYR A 83 PHE 0.016 0.002 PHE B 185 TRP 0.017 0.002 TRP C 108 HIS 0.011 0.002 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00801 (12783) covalent geometry : angle 0.97159 (17719) hydrogen bonds : bond 0.15777 ( 610) hydrogen bonds : angle 6.92843 ( 1652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9510 (mtp) cc_final: 0.9025 (mtp) REVERT: B 178 MET cc_start: 0.9498 (mtt) cc_final: 0.9126 (mtt) REVERT: B 184 ASN cc_start: 0.8938 (t0) cc_final: 0.8388 (t0) REVERT: C 178 MET cc_start: 0.9606 (mtp) cc_final: 0.9035 (mtp) REVERT: C 216 GLN cc_start: 0.9339 (tt0) cc_final: 0.8667 (pp30) REVERT: D 141 ILE cc_start: 0.8500 (mt) cc_final: 0.8285 (mp) REVERT: D 178 MET cc_start: 0.9515 (mtt) cc_final: 0.9141 (mtt) REVERT: D 184 ASN cc_start: 0.9063 (t0) cc_final: 0.8636 (t0) REVERT: D 243 TRP cc_start: 0.5367 (t60) cc_final: 0.4935 (t60) REVERT: P 226 TYR cc_start: 0.7426 (m-80) cc_final: 0.7034 (m-80) REVERT: P 231 ARG cc_start: 0.7668 (ttt90) cc_final: 0.7288 (ttp80) outliers start: 7 outliers final: 0 residues processed: 132 average time/residue: 0.1468 time to fit residues: 25.9142 Evaluate side-chains 76 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0060 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 44 GLN A 144 ASN B 183 HIS C 9 GLN C 27 ASN C 53 GLN C 183 HIS I 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.064753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.048767 restraints weight = 87481.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.050317 restraints weight = 47974.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.051358 restraints weight = 32554.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.052028 restraints weight = 25262.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.052363 restraints weight = 21541.003| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12783 Z= 0.155 Angle : 0.644 7.420 17719 Z= 0.374 Chirality : 0.048 0.219 1929 Planarity : 0.005 0.078 1900 Dihedral : 25.286 86.501 2576 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.28 % Allowed : 4.48 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -2.67 (0.21), residues: 1254 helix: -0.89 (0.21), residues: 475 sheet: -2.22 (0.29), residues: 268 loop : -2.22 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 231 TYR 0.021 0.001 TYR D 226 PHE 0.020 0.001 PHE A 100 TRP 0.034 0.001 TRP B 19 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00334 (12783) covalent geometry : angle 0.64426 (17719) hydrogen bonds : bond 0.05366 ( 610) hydrogen bonds : angle 5.35910 ( 1652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 178 MET cc_start: 0.9569 (mtp) cc_final: 0.9117 (mtp) REVERT: B 22 MET cc_start: 0.7633 (mtm) cc_final: 0.6996 (mmt) REVERT: B 178 MET cc_start: 0.9455 (mtt) cc_final: 0.8974 (mtm) REVERT: B 184 ASN cc_start: 0.9197 (t0) cc_final: 0.8612 (t0) REVERT: C 178 MET cc_start: 0.9693 (mtp) cc_final: 0.9146 (mtp) REVERT: C 184 ASN cc_start: 0.8855 (m-40) cc_final: 0.8616 (t0) REVERT: D 100 PHE cc_start: 0.8668 (t80) cc_final: 0.8147 (t80) REVERT: D 104 LEU cc_start: 0.9463 (mt) cc_final: 0.9243 (mt) REVERT: D 141 ILE cc_start: 0.8475 (mt) cc_final: 0.8160 (mm) REVERT: D 178 MET cc_start: 0.9463 (mtt) cc_final: 0.9155 (mtt) REVERT: D 184 ASN cc_start: 0.9175 (t0) cc_final: 0.8791 (t0) REVERT: D 243 TRP cc_start: 0.5224 (t60) cc_final: 0.4896 (t60) REVERT: I 221 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: M 226 TYR cc_start: 0.7771 (m-80) cc_final: 0.6904 (m-80) REVERT: P 230 SER cc_start: 0.8034 (m) cc_final: 0.7774 (p) outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 0.1208 time to fit residues: 18.5841 Evaluate side-chains 71 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 121 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.062095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045465 restraints weight = 88056.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.046916 restraints weight = 49278.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.047866 restraints weight = 33803.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.048527 restraints weight = 26674.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048861 restraints weight = 22710.142| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12783 Z= 0.181 Angle : 0.630 7.652 17719 Z= 0.365 Chirality : 0.046 0.205 1929 Planarity : 0.004 0.049 1900 Dihedral : 25.117 80.760 2576 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -2.21 (0.22), residues: 1254 helix: -0.18 (0.21), residues: 473 sheet: -2.25 (0.28), residues: 293 loop : -2.11 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 269 TYR 0.021 0.002 TYR D 226 PHE 0.011 0.001 PHE C 26 TRP 0.018 0.001 TRP D 108 HIS 0.007 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00387 (12783) covalent geometry : angle 0.63047 (17719) hydrogen bonds : bond 0.05574 ( 610) hydrogen bonds : angle 5.17944 ( 1652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.4661 (mpp) cc_final: 0.2935 (mpp) REVERT: A 85 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 150 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 178 MET cc_start: 0.9590 (mtp) cc_final: 0.9189 (mtp) REVERT: A 182 ILE cc_start: 0.9776 (mt) cc_final: 0.9541 (mt) REVERT: B 178 MET cc_start: 0.9420 (mtt) cc_final: 0.9047 (mtt) REVERT: B 184 ASN cc_start: 0.9177 (t0) cc_final: 0.8632 (t0) REVERT: C 178 MET cc_start: 0.9704 (mtp) cc_final: 0.9183 (mtp) REVERT: C 182 ILE cc_start: 0.9768 (mt) cc_final: 0.9549 (mt) REVERT: C 184 ASN cc_start: 0.8886 (m-40) cc_final: 0.8561 (t0) REVERT: D 20 ARG cc_start: 0.9073 (mtt-85) cc_final: 0.8856 (tpm170) REVERT: D 22 MET cc_start: 0.7664 (mtm) cc_final: 0.7129 (mtm) REVERT: D 100 PHE cc_start: 0.8659 (t80) cc_final: 0.8306 (t80) REVERT: D 104 LEU cc_start: 0.9433 (mt) cc_final: 0.9206 (mt) REVERT: D 141 ILE cc_start: 0.8506 (mt) cc_final: 0.8198 (mm) REVERT: D 184 ASN cc_start: 0.9132 (t0) cc_final: 0.8815 (t0) REVERT: D 243 TRP cc_start: 0.5390 (t60) cc_final: 0.4994 (t60) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1200 time to fit residues: 15.9007 Evaluate side-chains 70 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.0050 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 82 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS ** C 184 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 = 0.3688 r_free = 0.3688 target = 0.063746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047193 restraints weight = 86509.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.048759 restraints weight = 47779.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.049800 restraints weight = 32413.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050460 restraints weight = 25062.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.050788 restraints weight = 21358.998| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12783 Z= 0.134 Angle : 0.584 7.580 17719 Z= 0.337 Chirality : 0.045 0.165 1929 Planarity : 0.004 0.041 1900 Dihedral : 24.983 78.917 2576 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.75 (0.23), residues: 1254 helix: 0.35 (0.22), residues: 475 sheet: -2.10 (0.28), residues: 289 loop : -1.98 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 231 TYR 0.017 0.001 TYR D 226 PHE 0.010 0.001 PHE B 185 TRP 0.009 0.001 TRP C 108 HIS 0.007 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00287 (12783) covalent geometry : angle 0.58362 (17719) hydrogen bonds : bond 0.04226 ( 610) hydrogen bonds : angle 4.86685 ( 1652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9588 (mtp) cc_final: 0.9123 (mtp) REVERT: B 22 MET cc_start: 0.7948 (mtm) cc_final: 0.7380 (mtm) REVERT: B 178 MET cc_start: 0.9438 (mtt) cc_final: 0.9028 (mtt) REVERT: B 184 ASN cc_start: 0.9146 (t0) cc_final: 0.8574 (t0) REVERT: C 178 MET cc_start: 0.9703 (mtp) cc_final: 0.9140 (mtp) REVERT: D 20 ARG cc_start: 0.9080 (mtt-85) cc_final: 0.8857 (tpm170) REVERT: D 100 PHE cc_start: 0.8600 (t80) cc_final: 0.8156 (t80) REVERT: D 104 LEU cc_start: 0.9415 (mt) cc_final: 0.9166 (mt) REVERT: D 141 ILE cc_start: 0.8483 (mt) cc_final: 0.8176 (mm) REVERT: D 178 MET cc_start: 0.9463 (mtt) cc_final: 0.9129 (mtt) REVERT: D 184 ASN cc_start: 0.9144 (t0) cc_final: 0.8833 (t0) REVERT: D 243 TRP cc_start: 0.5453 (t60) cc_final: 0.5138 (t60) REVERT: J 268 ILE cc_start: 0.9510 (pt) cc_final: 0.9206 (mp) REVERT: M 226 TYR cc_start: 0.7586 (m-80) cc_final: 0.6636 (m-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1142 time to fit residues: 15.7858 Evaluate side-chains 67 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 114 HIS C 184 ASN D 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.061171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.044507 restraints weight = 89183.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.046011 restraints weight = 48661.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047036 restraints weight = 32886.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047638 restraints weight = 25503.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.047946 restraints weight = 21772.849| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12783 Z= 0.220 Angle : 0.642 9.441 17719 Z= 0.367 Chirality : 0.046 0.180 1929 Planarity : 0.005 0.075 1900 Dihedral : 25.026 85.073 2576 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.70 (0.23), residues: 1254 helix: 0.39 (0.22), residues: 483 sheet: -2.15 (0.28), residues: 280 loop : -1.94 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 228 TYR 0.022 0.002 TYR D 83 PHE 0.012 0.001 PHE C 26 TRP 0.015 0.002 TRP D 108 HIS 0.005 0.002 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00469 (12783) covalent geometry : angle 0.64218 (17719) hydrogen bonds : bond 0.05944 ( 610) hydrogen bonds : angle 5.05351 ( 1652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.5482 (mpp) cc_final: 0.5194 (mpp) REVERT: A 178 MET cc_start: 0.9598 (mtp) cc_final: 0.8678 (mtm) REVERT: A 182 ILE cc_start: 0.9763 (mt) cc_final: 0.9510 (mt) REVERT: B 184 ASN cc_start: 0.9067 (t0) cc_final: 0.8541 (t0) REVERT: C 73 ILE cc_start: 0.8105 (mt) cc_final: 0.7845 (mp) REVERT: C 178 MET cc_start: 0.9635 (mtp) cc_final: 0.9167 (mtp) REVERT: D 83 TYR cc_start: 0.7874 (t80) cc_final: 0.7439 (t80) REVERT: D 100 PHE cc_start: 0.8648 (t80) cc_final: 0.8142 (t80) REVERT: D 104 LEU cc_start: 0.9410 (mt) cc_final: 0.9167 (mt) REVERT: D 141 ILE cc_start: 0.8434 (mt) cc_final: 0.8112 (mm) REVERT: D 184 ASN cc_start: 0.9100 (t0) cc_final: 0.8781 (t0) REVERT: D 243 TRP cc_start: 0.5591 (t60) cc_final: 0.5365 (t60) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1093 time to fit residues: 13.2283 Evaluate side-chains 65 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 22 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.063324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046358 restraints weight = 85410.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.048025 restraints weight = 45953.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.049127 restraints weight = 30712.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.049758 restraints weight = 23547.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050260 restraints weight = 20030.913| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12783 Z= 0.129 Angle : 0.579 7.765 17719 Z= 0.331 Chirality : 0.045 0.177 1929 Planarity : 0.004 0.043 1900 Dihedral : 24.898 77.286 2576 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1254 helix: 0.63 (0.22), residues: 484 sheet: -2.02 (0.28), residues: 293 loop : -1.88 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 107 TYR 0.022 0.001 TYR D 83 PHE 0.020 0.001 PHE A 100 TRP 0.015 0.001 TRP D 108 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00278 (12783) covalent geometry : angle 0.57908 (17719) hydrogen bonds : bond 0.04028 ( 610) hydrogen bonds : angle 4.75446 ( 1652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 178 MET cc_start: 0.9599 (mtp) cc_final: 0.8647 (mtm) REVERT: A 182 ILE cc_start: 0.9760 (mt) cc_final: 0.9551 (mt) REVERT: A 216 GLN cc_start: 0.9131 (tt0) cc_final: 0.8877 (tp40) REVERT: B 178 MET cc_start: 0.9431 (mtt) cc_final: 0.9054 (mtt) REVERT: B 184 ASN cc_start: 0.9094 (t0) cc_final: 0.8599 (t0) REVERT: C 73 ILE cc_start: 0.8066 (mt) cc_final: 0.7844 (mp) REVERT: C 178 MET cc_start: 0.9628 (mtp) cc_final: 0.9116 (mtp) REVERT: D 100 PHE cc_start: 0.8623 (t80) cc_final: 0.8105 (t80) REVERT: D 104 LEU cc_start: 0.9391 (mt) cc_final: 0.9152 (mt) REVERT: D 141 ILE cc_start: 0.8343 (mt) cc_final: 0.8005 (mm) REVERT: D 178 MET cc_start: 0.9459 (mtt) cc_final: 0.9127 (mtt) REVERT: D 184 ASN cc_start: 0.9094 (t0) cc_final: 0.8826 (t0) REVERT: D 243 TRP cc_start: 0.5582 (t60) cc_final: 0.5280 (t60) REVERT: D 255 SER cc_start: 0.7922 (p) cc_final: 0.7701 (m) REVERT: J 268 ILE cc_start: 0.9478 (pt) cc_final: 0.9178 (mp) REVERT: M 226 TYR cc_start: 0.7609 (m-80) cc_final: 0.6760 (m-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1106 time to fit residues: 15.6629 Evaluate side-chains 73 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.063834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047486 restraints weight = 89827.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049045 restraints weight = 48904.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.050117 restraints weight = 33170.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.050653 restraints weight = 25694.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.051169 restraints weight = 22286.498| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12783 Z= 0.156 Angle : 0.595 8.849 17719 Z= 0.338 Chirality : 0.044 0.171 1929 Planarity : 0.004 0.039 1900 Dihedral : 24.821 80.180 2576 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1254 helix: 0.78 (0.22), residues: 482 sheet: -1.88 (0.29), residues: 283 loop : -1.85 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 107 TYR 0.014 0.001 TYR D 226 PHE 0.018 0.001 PHE A 100 TRP 0.016 0.001 TRP D 108 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00337 (12783) covalent geometry : angle 0.59538 (17719) hydrogen bonds : bond 0.04530 ( 610) hydrogen bonds : angle 4.77811 ( 1652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 178 MET cc_start: 0.9643 (mtp) cc_final: 0.8694 (mtm) REVERT: A 182 ILE cc_start: 0.9786 (mt) cc_final: 0.9503 (mt) REVERT: A 216 GLN cc_start: 0.9104 (tt0) cc_final: 0.8860 (tp40) REVERT: B 178 MET cc_start: 0.9437 (mtt) cc_final: 0.9187 (mtt) REVERT: B 184 ASN cc_start: 0.9151 (t0) cc_final: 0.8650 (t0) REVERT: C 178 MET cc_start: 0.9652 (mtp) cc_final: 0.9158 (mtp) REVERT: D 22 MET cc_start: 0.7552 (mtt) cc_final: 0.7044 (mmm) REVERT: D 141 ILE cc_start: 0.8389 (mt) cc_final: 0.8058 (mm) REVERT: D 178 MET cc_start: 0.9429 (mtt) cc_final: 0.9086 (mtt) REVERT: D 184 ASN cc_start: 0.9134 (t0) cc_final: 0.8868 (t0) REVERT: D 243 TRP cc_start: 0.5544 (t60) cc_final: 0.5306 (t60) REVERT: D 255 SER cc_start: 0.7938 (p) cc_final: 0.7720 (m) REVERT: J 268 ILE cc_start: 0.9469 (pt) cc_final: 0.9162 (mp) REVERT: M 226 TYR cc_start: 0.7819 (m-80) cc_final: 0.7067 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0945 time to fit residues: 12.9415 Evaluate side-chains 69 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** 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 = 0.3663 r_free = 0.3663 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047313 restraints weight = 89763.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048826 restraints weight = 48863.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.049881 restraints weight = 33279.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.050556 restraints weight = 25802.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050882 restraints weight = 22012.434| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12783 Z= 0.165 Angle : 0.597 8.154 17719 Z= 0.339 Chirality : 0.044 0.168 1929 Planarity : 0.004 0.039 1900 Dihedral : 24.776 81.792 2576 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.27 (0.23), residues: 1254 helix: 0.85 (0.22), residues: 483 sheet: -1.96 (0.28), residues: 283 loop : -1.79 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.032 0.001 TYR D 83 PHE 0.011 0.001 PHE A 100 TRP 0.016 0.001 TRP D 108 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00356 (12783) covalent geometry : angle 0.59655 (17719) hydrogen bonds : bond 0.04593 ( 610) hydrogen bonds : angle 4.78762 ( 1652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9640 (mtp) cc_final: 0.8656 (mtm) REVERT: A 182 ILE cc_start: 0.9780 (mt) cc_final: 0.9497 (mt) REVERT: A 216 GLN cc_start: 0.9114 (tt0) cc_final: 0.8891 (tp40) REVERT: B 178 MET cc_start: 0.9434 (mtt) cc_final: 0.9057 (mtt) REVERT: B 184 ASN cc_start: 0.9114 (t0) cc_final: 0.8595 (t0) REVERT: C 178 MET cc_start: 0.9646 (mtp) cc_final: 0.9160 (mtp) REVERT: D 22 MET cc_start: 0.7669 (mtt) cc_final: 0.7033 (mpp) REVERT: D 141 ILE cc_start: 0.8400 (mt) cc_final: 0.8064 (mm) REVERT: D 154 MET cc_start: 0.8671 (mtm) cc_final: 0.8274 (mtm) REVERT: D 178 MET cc_start: 0.9432 (mtt) cc_final: 0.9153 (mtt) REVERT: D 184 ASN cc_start: 0.9134 (t0) cc_final: 0.8876 (t0) REVERT: D 243 TRP cc_start: 0.5629 (t60) cc_final: 0.5359 (t60) REVERT: D 255 SER cc_start: 0.7909 (p) cc_final: 0.7688 (m) REVERT: J 258 LYS cc_start: 0.9206 (mttt) cc_final: 0.8763 (mtmm) REVERT: J 268 ILE cc_start: 0.9465 (pt) cc_final: 0.9138 (mp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1039 time to fit residues: 13.7657 Evaluate side-chains 69 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 131 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 overall best weight: 0.3552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** 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 = 0.3702 r_free = 0.3702 target = 0.065222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048914 restraints weight = 86488.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.050501 restraints weight = 47091.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.051596 restraints weight = 31754.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.052164 restraints weight = 24553.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.052579 restraints weight = 21142.535| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12783 Z= 0.125 Angle : 0.580 7.345 17719 Z= 0.326 Chirality : 0.044 0.193 1929 Planarity : 0.004 0.041 1900 Dihedral : 24.642 75.311 2576 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.17 (0.24), residues: 1254 helix: 0.94 (0.23), residues: 483 sheet: -1.85 (0.28), residues: 293 loop : -1.78 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 107 TYR 0.019 0.001 TYR D 83 PHE 0.016 0.001 PHE A 100 TRP 0.010 0.001 TRP C 108 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00269 (12783) covalent geometry : angle 0.57974 (17719) hydrogen bonds : bond 0.03687 ( 610) hydrogen bonds : angle 4.64564 ( 1652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7476 (tm-30) REVERT: A 178 MET cc_start: 0.9628 (mtp) cc_final: 0.8574 (mtm) REVERT: A 216 GLN cc_start: 0.9135 (tt0) cc_final: 0.8933 (tp40) REVERT: B 178 MET cc_start: 0.9457 (mtt) cc_final: 0.9093 (mtt) REVERT: B 184 ASN cc_start: 0.9103 (t0) cc_final: 0.8591 (t0) REVERT: C 178 MET cc_start: 0.9628 (mtp) cc_final: 0.9111 (mtp) REVERT: C 258 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8667 (pttm) REVERT: D 141 ILE cc_start: 0.8388 (mt) cc_final: 0.8055 (mm) REVERT: D 178 MET cc_start: 0.9436 (mtt) cc_final: 0.9059 (mtt) REVERT: D 243 TRP cc_start: 0.5664 (t60) cc_final: 0.5444 (t60) REVERT: D 255 SER cc_start: 0.7978 (p) cc_final: 0.7757 (m) REVERT: I 268 ILE cc_start: 0.9520 (pt) cc_final: 0.9138 (mp) REVERT: J 258 LYS cc_start: 0.9198 (mttt) cc_final: 0.8709 (mtmm) REVERT: J 268 ILE cc_start: 0.9453 (pt) cc_final: 0.9124 (mp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1138 time to fit residues: 15.6719 Evaluate side-chains 68 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 38 optimal weight: 0.0870 chunk 100 optimal weight: 0.6980 chunk 14 optimal weight: 0.0570 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS C 53 GLN D 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.066155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.049763 restraints weight = 87333.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.051393 restraints weight = 46871.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.052565 restraints weight = 31376.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053265 restraints weight = 24104.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.053624 restraints weight = 20377.439| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12783 Z= 0.123 Angle : 0.576 6.898 17719 Z= 0.324 Chirality : 0.044 0.145 1929 Planarity : 0.004 0.040 1900 Dihedral : 24.460 75.313 2576 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.06 (0.24), residues: 1254 helix: 1.05 (0.23), residues: 483 sheet: -1.75 (0.28), residues: 294 loop : -1.76 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 107 TYR 0.015 0.001 TYR D 83 PHE 0.011 0.001 PHE C 100 TRP 0.023 0.001 TRP D 108 HIS 0.011 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00265 (12783) covalent geometry : angle 0.57649 (17719) hydrogen bonds : bond 0.03440 ( 610) hydrogen bonds : angle 4.52373 ( 1652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 178 MET cc_start: 0.9639 (mtp) cc_final: 0.8631 (mtm) REVERT: A 182 ILE cc_start: 0.9783 (mt) cc_final: 0.9559 (mt) REVERT: A 216 GLN cc_start: 0.9122 (tt0) cc_final: 0.8908 (tp40) REVERT: B 154 MET cc_start: 0.8415 (mtm) cc_final: 0.8000 (ptp) REVERT: B 184 ASN cc_start: 0.9101 (t0) cc_final: 0.8619 (t0) REVERT: C 108 TRP cc_start: 0.8346 (m100) cc_final: 0.8032 (m100) REVERT: C 178 MET cc_start: 0.9621 (mtp) cc_final: 0.9109 (mtp) REVERT: C 182 ILE cc_start: 0.9784 (mt) cc_final: 0.9551 (mt) REVERT: C 258 LYS cc_start: 0.9044 (ptmt) cc_final: 0.8668 (pttp) REVERT: D 22 MET cc_start: 0.7629 (mtt) cc_final: 0.7116 (mpp) REVERT: D 141 ILE cc_start: 0.8514 (mt) cc_final: 0.8193 (mm) REVERT: D 154 MET cc_start: 0.8488 (mtm) cc_final: 0.8044 (mtm) REVERT: D 178 MET cc_start: 0.9413 (mtt) cc_final: 0.9082 (mtt) REVERT: D 243 TRP cc_start: 0.5723 (t60) cc_final: 0.5437 (t60) REVERT: D 255 SER cc_start: 0.7911 (p) cc_final: 0.7684 (m) REVERT: I 268 ILE cc_start: 0.9499 (pt) cc_final: 0.9122 (mp) REVERT: J 258 LYS cc_start: 0.9216 (mttt) cc_final: 0.8834 (mtmm) REVERT: J 268 ILE cc_start: 0.9447 (pt) cc_final: 0.9163 (mp) REVERT: M 226 TYR cc_start: 0.7452 (m-80) cc_final: 0.7025 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1091 time to fit residues: 15.6541 Evaluate side-chains 70 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 25 optimal weight: 7.9990 chunk 55 optimal weight: 0.0470 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.066079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.049726 restraints weight = 86631.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.051358 restraints weight = 46318.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052500 restraints weight = 30965.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.053224 restraints weight = 23830.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.053432 restraints weight = 20179.114| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12783 Z= 0.120 Angle : 0.565 7.124 17719 Z= 0.316 Chirality : 0.043 0.156 1929 Planarity : 0.004 0.042 1900 Dihedral : 24.297 75.600 2576 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.24), residues: 1254 helix: 1.11 (0.23), residues: 483 sheet: -1.64 (0.28), residues: 295 loop : -1.68 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.028 0.001 TYR D 83 PHE 0.012 0.001 PHE C 185 TRP 0.011 0.001 TRP B 108 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00259 (12783) covalent geometry : angle 0.56533 (17719) hydrogen bonds : bond 0.03359 ( 610) hydrogen bonds : angle 4.43263 ( 1652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.26 seconds wall clock time: 38 minutes 15.34 seconds (2295.34 seconds total)