Starting phenix.real_space_refine on Fri Sep 11 23:38:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vdk_21151/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vdk_21151/09_2026/6vdk_21151.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.75, per 1000 atoms: 0.22 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: 0.98 Conformation dependent library (CDL) restraints added in 448.5 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: 1.60 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: 1.93 Time building geometry restraints manager: 1.33 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: 17177 2.57 - 5.14: 489 5.14 - 7.70: 39 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=" O4' DC E 38 " pdb=" C1' DC E 38 " pdb=" N1 DC E 38 " ideal model delta sigma weight residual 108.00 113.10 -5.10 7.00e-01 2.04e+00 5.31e+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 - 0.060: 1419 0.060 - 0.120: 426 0.120 - 0.180: 75 0.180 - 0.239: 6 0.239 - 0.299: 3 Chirality restraints: 1929 Sorted by residual: 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 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 2.43 2.16 0.27 2.00e-01 2.50e+01 1.79e+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 2.43 2.17 0.26 2.00e-01 2.50e+01 1.69e+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: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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= 0.542 Angle : 1.019 12.840 17719 Z= 0.750 Chirality : 0.057 0.299 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/Z covalent geometry : bond 0.00827 / 0.54 (12783) covalent geometry : angle 1.01871 / 0.75 (17719) hydrogen bonds : bond 0.15777 / 10.68 ( 610) hydrogen bonds : angle 6.92843 / 4.93 ( 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 : 0.410 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: 0.1320 time to fit residues: 23.7578 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 : 0.408 ------------------------------------------------------------------------------- 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: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.2980 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: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 HIS A 44 GLN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN B 183 HIS C 27 ASN C 53 GLN C 183 HIS I 221 GLN J 274 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.064433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.048488 restraints weight = 88615.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.049968 restraints weight = 48606.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.051011 restraints weight = 33044.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.051611 restraints weight = 25812.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.052086 restraints weight = 22172.581| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 12783 Z= 0.156 Angle : 0.728 7.704 17719 Z= 0.416 Chirality : 0.056 0.266 1929 Planarity : 0.006 0.119 1900 Dihedral : 25.738 86.102 2576 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % 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: -2.87 (0.21), residues: 1254 helix: -1.18 (0.20), residues: 470 sheet: -2.14 (0.30), residues: 262 loop : -2.32 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 228 TYR 0.019 0.002 TYR D 226 PHE 0.020 0.002 PHE A 100 TRP 0.033 0.001 TRP B 19 HIS 0.006 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (12783) covalent geometry : angle 0.72787 / 0.42 (17719) hydrogen bonds : bond 0.06917 / 4.67 ( 610) hydrogen bonds : angle 5.72354 / 4.06 ( 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 101 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9523 (mtp) cc_final: 0.9096 (mtp) REVERT: B 22 MET cc_start: 0.7687 (mtm) cc_final: 0.7100 (mtm) REVERT: B 178 MET cc_start: 0.9477 (mtt) cc_final: 0.9134 (mtt) REVERT: B 184 ASN cc_start: 0.9172 (t0) cc_final: 0.8579 (t0) REVERT: C 178 MET cc_start: 0.9657 (mtp) cc_final: 0.9121 (mtp) REVERT: D 22 MET cc_start: 0.7459 (mtm) cc_final: 0.7121 (mtm) REVERT: D 100 PHE cc_start: 0.8647 (t80) cc_final: 0.8270 (t80) REVERT: D 104 LEU cc_start: 0.9453 (mt) cc_final: 0.9233 (mt) REVERT: D 141 ILE cc_start: 0.8524 (mt) cc_final: 0.8226 (mm) REVERT: D 178 MET cc_start: 0.9465 (mtt) cc_final: 0.9153 (mtt) REVERT: D 184 ASN cc_start: 0.9167 (t0) cc_final: 0.8786 (t0) REVERT: D 243 TRP cc_start: 0.5191 (t60) cc_final: 0.4840 (t60) REVERT: I 221 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6936 (pm20) REVERT: M 226 TYR cc_start: 0.7626 (m-80) cc_final: 0.6979 (m-80) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1166 time to fit residues: 16.9440 Evaluate side-chains 68 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 HIS ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 252 GLN B 18 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 = 0.3641 r_free = 0.3641 target = 0.062793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046860 restraints weight = 91007.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048302 restraints weight = 50769.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.049323 restraints weight = 34896.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049957 restraints weight = 27243.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.050288 restraints weight = 23277.484| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1955 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= 0.177 Angle : 0.688 8.265 17719 Z= 0.395 Chirality : 0.052 0.254 1929 Planarity : 0.005 0.056 1900 Dihedral : 25.487 80.492 2576 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.17 % 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: -2.37 (0.22), residues: 1254 helix: -0.38 (0.21), residues: 472 sheet: -2.30 (0.29), residues: 279 loop : -2.17 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 228 TYR 0.019 0.002 TYR D 226 PHE 0.012 0.001 PHE A 100 TRP 0.014 0.001 TRP B 19 HIS 0.008 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (12783) covalent geometry : angle 0.68847 / 0.40 (17719) hydrogen bonds : bond 0.06631 / 4.40 ( 610) hydrogen bonds : angle 5.39847 / 3.84 ( 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 88 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 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: 0.7882 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 154 MET cc_start: 0.9206 (mmp) cc_final: 0.9004 (mmp) REVERT: A 178 MET cc_start: 0.9608 (mtp) cc_final: 0.9239 (mtp) REVERT: A 182 ILE cc_start: 0.9783 (mt) cc_final: 0.9527 (mt) REVERT: A 184 ASN cc_start: 0.9415 (m-40) cc_final: 0.8766 (t0) REVERT: B 22 MET cc_start: 0.7708 (mtm) cc_final: 0.7226 (mmt) REVERT: B 184 ASN cc_start: 0.9181 (t0) cc_final: 0.8589 (t0) REVERT: C 62 GLN cc_start: 0.9102 (mt0) cc_final: 0.8865 (mt0) REVERT: C 178 MET cc_start: 0.9705 (mtp) cc_final: 0.9206 (mtp) REVERT: C 182 ILE cc_start: 0.9774 (mt) cc_final: 0.9571 (mt) REVERT: D 22 MET cc_start: 0.7596 (mtm) cc_final: 0.7353 (mtm) REVERT: D 141 ILE cc_start: 0.8549 (mt) cc_final: 0.8253 (mm) REVERT: D 184 ASN cc_start: 0.9175 (t0) cc_final: 0.8784 (t0) REVERT: D 243 TRP cc_start: 0.5297 (t60) cc_final: 0.4960 (t60) outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 0.1026 time to fit residues: 13.4608 Evaluate side-chains 65 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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: 0.0670 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 82 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 121 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 HIS A 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.063757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047165 restraints weight = 88278.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.048706 restraints weight = 49299.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049759 restraints weight = 33690.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050308 restraints weight = 26236.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.050825 restraints weight = 22604.411| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12783 Z= 0.124 Angle : 0.629 7.516 17719 Z= 0.359 Chirality : 0.051 0.228 1929 Planarity : 0.004 0.048 1900 Dihedral : 25.267 78.012 2576 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -2.02 (0.22), residues: 1254 helix: 0.06 (0.22), residues: 473 sheet: -2.14 (0.28), residues: 291 loop : -2.10 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.015 0.001 TYR D 226 PHE 0.012 0.001 PHE M 223 TRP 0.010 0.001 TRP D 235 HIS 0.007 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (12783) covalent geometry : angle 0.62940 / 0.36 (17719) hydrogen bonds : bond 0.04949 / 3.32 ( 610) hydrogen bonds : angle 5.02211 / 3.55 ( 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 95 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 178 MET cc_start: 0.9562 (mtp) cc_final: 0.9075 (mtp) REVERT: A 182 ILE cc_start: 0.9758 (mt) cc_final: 0.9555 (mt) REVERT: A 184 ASN cc_start: 0.9361 (m-40) cc_final: 0.8665 (t0) REVERT: B 22 MET cc_start: 0.7868 (mtm) cc_final: 0.7499 (mmt) REVERT: B 178 MET cc_start: 0.9468 (mtt) cc_final: 0.9140 (mtt) REVERT: B 184 ASN cc_start: 0.9128 (t0) cc_final: 0.8595 (t0) REVERT: C 62 GLN cc_start: 0.8942 (mt0) cc_final: 0.8731 (mt0) REVERT: C 73 ILE cc_start: 0.8074 (mt) cc_final: 0.7860 (mp) REVERT: C 178 MET cc_start: 0.9676 (mtp) cc_final: 0.9117 (mtp) REVERT: D 100 PHE cc_start: 0.8501 (t80) cc_final: 0.8130 (t80) REVERT: D 141 ILE cc_start: 0.8451 (mt) cc_final: 0.8136 (mm) REVERT: D 178 MET cc_start: 0.9465 (mtt) cc_final: 0.9139 (mtt) REVERT: D 184 ASN cc_start: 0.9134 (t0) cc_final: 0.8767 (t0) REVERT: D 243 TRP cc_start: 0.5397 (t60) cc_final: 0.5033 (t60) REVERT: J 268 ILE cc_start: 0.9497 (pt) cc_final: 0.9213 (mp) REVERT: M 226 TYR cc_start: 0.7538 (m-80) cc_final: 0.6623 (m-80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1083 time to fit residues: 14.7190 Evaluate side-chains 66 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 0.4980 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 HIS ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 114 HIS J 274 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.062668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.046494 restraints weight = 91347.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047941 restraints weight = 50582.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.048992 restraints weight = 34673.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.049538 restraints weight = 27021.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.050027 restraints weight = 23350.795| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12783 Z= 0.181 Angle : 0.672 8.424 17719 Z= 0.378 Chirality : 0.050 0.225 1929 Planarity : 0.004 0.041 1900 Dihedral : 25.241 80.962 2576 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -1.84 (0.23), residues: 1254 helix: 0.28 (0.22), residues: 476 sheet: -2.14 (0.29), residues: 281 loop : -2.05 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 107 TYR 0.014 0.001 TYR D 226 PHE 0.010 0.001 PHE C 26 TRP 0.013 0.001 TRP B 61 HIS 0.005 0.002 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (12783) covalent geometry : angle 0.67187 / 0.38 (17719) hydrogen bonds : bond 0.06406 / 4.22 ( 610) hydrogen bonds : angle 5.09067 / 3.61 ( 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 81 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9626 (mtp) cc_final: 0.9221 (mtp) REVERT: A 182 ILE cc_start: 0.9790 (mt) cc_final: 0.9529 (mt) REVERT: A 184 ASN cc_start: 0.9486 (m-40) cc_final: 0.8888 (t0) REVERT: B 184 ASN cc_start: 0.9179 (t0) cc_final: 0.8586 (t0) REVERT: C 73 ILE cc_start: 0.8073 (mt) cc_final: 0.7830 (mp) REVERT: C 178 MET cc_start: 0.9638 (mtp) cc_final: 0.9160 (mtp) REVERT: C 182 ILE cc_start: 0.9775 (mt) cc_final: 0.9555 (mt) REVERT: D 100 PHE cc_start: 0.8662 (t80) cc_final: 0.8207 (t80) REVERT: D 141 ILE cc_start: 0.8532 (mt) cc_final: 0.8218 (mm) REVERT: D 184 ASN cc_start: 0.9132 (t0) cc_final: 0.8754 (t0) REVERT: D 243 TRP cc_start: 0.5482 (t60) cc_final: 0.5103 (t60) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0993 time to fit residues: 12.6671 Evaluate side-chains 63 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 0.0970 chunk 58 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.063790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.047493 restraints weight = 89099.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049030 restraints weight = 49241.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050125 restraints weight = 33601.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050770 restraints weight = 26061.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.051126 restraints weight = 22146.380| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12783 Z= 0.132 Angle : 0.623 7.753 17719 Z= 0.352 Chirality : 0.050 0.220 1929 Planarity : 0.004 0.050 1900 Dihedral : 25.196 80.783 2576 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: -1.68 (0.23), residues: 1254 helix: 0.39 (0.22), residues: 477 sheet: -2.00 (0.29), residues: 281 loop : -2.00 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.015 0.001 TYR D 226 PHE 0.012 0.001 PHE C 100 TRP 0.011 0.001 TRP C 108 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (12783) covalent geometry : angle 0.62330 / 0.35 (17719) hydrogen bonds : bond 0.04846 / 3.22 ( 610) hydrogen bonds : angle 4.91916 / 3.49 ( 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 86 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 178 MET cc_start: 0.9626 (mtp) cc_final: 0.8710 (mtm) REVERT: A 182 ILE cc_start: 0.9775 (mt) cc_final: 0.9495 (mt) REVERT: A 184 ASN cc_start: 0.9487 (m-40) cc_final: 0.8849 (t0) REVERT: A 216 GLN cc_start: 0.9139 (tt0) cc_final: 0.8867 (tp40) REVERT: B 22 MET cc_start: 0.7888 (mtm) cc_final: 0.7345 (mtm) REVERT: B 178 MET cc_start: 0.9442 (mtt) cc_final: 0.9104 (mtt) REVERT: B 184 ASN cc_start: 0.9208 (t0) cc_final: 0.8677 (t0) REVERT: C 73 ILE cc_start: 0.8013 (mt) cc_final: 0.7756 (mp) REVERT: C 178 MET cc_start: 0.9627 (mtp) cc_final: 0.9129 (mtp) REVERT: C 182 ILE cc_start: 0.9765 (mt) cc_final: 0.9540 (mt) REVERT: D 100 PHE cc_start: 0.8638 (t80) cc_final: 0.8212 (t80) REVERT: D 141 ILE cc_start: 0.8467 (mt) cc_final: 0.8156 (mm) REVERT: D 178 MET cc_start: 0.9428 (mtt) cc_final: 0.9076 (mtt) REVERT: D 184 ASN cc_start: 0.9126 (t0) cc_final: 0.8790 (t0) REVERT: D 243 TRP cc_start: 0.5451 (t60) cc_final: 0.5123 (t60) REVERT: D 255 SER cc_start: 0.7970 (p) cc_final: 0.7755 (m) REVERT: J 268 ILE cc_start: 0.9474 (pt) cc_final: 0.9183 (mp) REVERT: M 226 TYR cc_start: 0.7843 (m-80) cc_final: 0.7014 (m-80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0990 time to fit residues: 13.3162 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 : 0.412 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN D 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.063316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047103 restraints weight = 89166.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048656 restraints weight = 49091.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.049707 restraints weight = 33382.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.050250 restraints weight = 25917.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.050644 restraints weight = 22349.871| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2767 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= 0.145 Angle : 0.627 8.055 17719 Z= 0.352 Chirality : 0.049 0.217 1929 Planarity : 0.004 0.046 1900 Dihedral : 25.158 84.081 2576 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -1.58 (0.23), residues: 1254 helix: 0.49 (0.22), residues: 481 sheet: -2.03 (0.29), residues: 281 loop : -1.92 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.014 0.001 TYR D 226 PHE 0.010 0.001 PHE C 26 TRP 0.012 0.001 TRP D 19 HIS 0.005 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12783) covalent geometry : angle 0.62701 / 0.35 (17719) hydrogen bonds : bond 0.05191 / 3.42 ( 610) hydrogen bonds : angle 4.87779 / 3.46 ( 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 89 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9625 (mtp) cc_final: 0.8663 (mtm) REVERT: A 182 ILE cc_start: 0.9785 (mt) cc_final: 0.9506 (mt) REVERT: A 184 ASN cc_start: 0.9491 (m-40) cc_final: 0.8833 (t0) REVERT: A 216 GLN cc_start: 0.9144 (tt0) cc_final: 0.8874 (tp40) REVERT: B 178 MET cc_start: 0.9434 (mtt) cc_final: 0.9178 (mtt) REVERT: B 184 ASN cc_start: 0.9147 (t0) cc_final: 0.8631 (t0) REVERT: C 73 ILE cc_start: 0.8062 (mt) cc_final: 0.7793 (mp) REVERT: C 178 MET cc_start: 0.9647 (mtp) cc_final: 0.9176 (mtp) REVERT: D 100 PHE cc_start: 0.8605 (t80) cc_final: 0.8176 (t80) REVERT: D 141 ILE cc_start: 0.8443 (mt) cc_final: 0.8124 (mm) REVERT: D 184 ASN cc_start: 0.9109 (t0) cc_final: 0.8782 (t0) REVERT: D 243 TRP cc_start: 0.5573 (t60) cc_final: 0.5280 (t60) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1012 time to fit residues: 13.7137 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 : 0.458 ------------------------------------------------------------------------------- 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: 0.5980 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 55 optimal weight: 0.0070 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.064780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048457 restraints weight = 87475.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.050038 restraints weight = 47608.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.051117 restraints weight = 32208.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.051692 restraints weight = 25029.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.052096 restraints weight = 21542.110| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12783 Z= 0.116 Angle : 0.610 8.620 17719 Z= 0.340 Chirality : 0.049 0.215 1929 Planarity : 0.004 0.069 1900 Dihedral : 24.988 79.403 2576 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.44 (0.23), residues: 1254 helix: 0.66 (0.22), residues: 481 sheet: -1.90 (0.29), residues: 273 loop : -1.95 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 231 TYR 0.013 0.001 TYR D 226 PHE 0.016 0.001 PHE C 100 TRP 0.013 0.001 TRP C 108 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (12783) covalent geometry : angle 0.60983 / 0.34 (17719) hydrogen bonds : bond 0.04233 / 2.82 ( 610) hydrogen bonds : angle 4.72579 / 3.34 ( 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 97 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 178 MET cc_start: 0.9622 (mtp) cc_final: 0.8595 (mtm) REVERT: A 182 ILE cc_start: 0.9778 (mt) cc_final: 0.9537 (mt) REVERT: A 184 ASN cc_start: 0.9467 (m-40) cc_final: 0.8759 (t0) REVERT: A 216 GLN cc_start: 0.9123 (tt0) cc_final: 0.8885 (tp40) REVERT: B 22 MET cc_start: 0.7836 (mtm) cc_final: 0.7299 (mtm) REVERT: B 178 MET cc_start: 0.9445 (mtt) cc_final: 0.9072 (mtt) REVERT: B 184 ASN cc_start: 0.9166 (t0) cc_final: 0.8643 (t0) REVERT: C 73 ILE cc_start: 0.8033 (mt) cc_final: 0.7802 (mp) REVERT: C 178 MET cc_start: 0.9631 (mtp) cc_final: 0.9142 (mtp) REVERT: D 100 PHE cc_start: 0.8605 (t80) cc_final: 0.8100 (t80) REVERT: D 141 ILE cc_start: 0.8401 (mt) cc_final: 0.8079 (mm) REVERT: D 178 MET cc_start: 0.9456 (mtt) cc_final: 0.9099 (mtt) REVERT: D 184 ASN cc_start: 0.9101 (t0) cc_final: 0.8824 (t0) REVERT: D 243 TRP cc_start: 0.5544 (t60) cc_final: 0.5236 (t60) REVERT: J 268 ILE cc_start: 0.9424 (pt) cc_final: 0.9152 (mp) REVERT: M 226 TYR cc_start: 0.7730 (m-80) cc_final: 0.6845 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1055 time to fit residues: 15.4312 Evaluate side-chains 74 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 0.5980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3641 r_free = 0.3641 target = 0.062781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046569 restraints weight = 90196.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048066 restraints weight = 49910.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049101 restraints weight = 34203.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.049647 restraints weight = 26680.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.050133 restraints weight = 23070.067| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12783 Z= 0.187 Angle : 0.661 8.437 17719 Z= 0.368 Chirality : 0.049 0.213 1929 Planarity : 0.004 0.044 1900 Dihedral : 25.002 87.996 2576 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.44 (0.23), residues: 1254 helix: 0.66 (0.22), residues: 483 sheet: -1.99 (0.29), residues: 281 loop : -1.88 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 107 TYR 0.012 0.001 TYR D 226 PHE 0.023 0.001 PHE A 100 TRP 0.014 0.001 TRP B 61 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (12783) covalent geometry : angle 0.66085 / 0.37 (17719) hydrogen bonds : bond 0.05761 / 3.80 ( 610) hydrogen bonds : angle 4.91181 / 3.48 ( 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 82 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9641 (mtp) cc_final: 0.8621 (mtm) REVERT: A 182 ILE cc_start: 0.9788 (mt) cc_final: 0.9489 (mt) REVERT: A 184 ASN cc_start: 0.9475 (m-40) cc_final: 0.8855 (t0) REVERT: A 216 GLN cc_start: 0.9123 (tt0) cc_final: 0.8891 (tp40) REVERT: B 154 MET cc_start: 0.8422 (mtm) cc_final: 0.8108 (ptp) REVERT: B 184 ASN cc_start: 0.9138 (t0) cc_final: 0.8621 (t0) REVERT: C 73 ILE cc_start: 0.8060 (mt) cc_final: 0.7792 (mp) REVERT: C 178 MET cc_start: 0.9651 (mtp) cc_final: 0.9187 (mtp) REVERT: D 100 PHE cc_start: 0.8675 (t80) cc_final: 0.8203 (t80) REVERT: D 141 ILE cc_start: 0.8457 (mt) cc_final: 0.8138 (mm) REVERT: D 184 ASN cc_start: 0.9133 (t0) cc_final: 0.8812 (t0) REVERT: D 243 TRP cc_start: 0.5541 (t60) cc_final: 0.5263 (t60) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1020 time to fit residues: 12.8744 Evaluate side-chains 66 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 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: 0.9990 chunk 100 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.063112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046390 restraints weight = 85104.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.047983 restraints weight = 46235.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049050 restraints weight = 31143.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049664 restraints weight = 24041.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.050141 restraints weight = 20517.239| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12783 Z= 0.117 Angle : 0.611 7.446 17719 Z= 0.341 Chirality : 0.048 0.213 1929 Planarity : 0.004 0.050 1900 Dihedral : 24.833 81.743 2576 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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: -1.30 (0.23), residues: 1254 helix: 0.81 (0.22), residues: 482 sheet: -1.84 (0.29), residues: 285 loop : -1.90 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 107 TYR 0.012 0.001 TYR D 226 PHE 0.031 0.001 PHE A 100 TRP 0.010 0.001 TRP D 235 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (12783) covalent geometry : angle 0.61076 / 0.34 (17719) hydrogen bonds : bond 0.04233 / 2.82 ( 610) hydrogen bonds : angle 4.75471 / 3.36 ( 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 92 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 178 MET cc_start: 0.9616 (mtp) cc_final: 0.8544 (mtm) REVERT: A 184 ASN cc_start: 0.9445 (m-40) cc_final: 0.8756 (t0) REVERT: A 216 GLN cc_start: 0.9138 (tt0) cc_final: 0.8937 (tp40) REVERT: B 178 MET cc_start: 0.9437 (mtt) cc_final: 0.9091 (mtt) REVERT: B 184 ASN cc_start: 0.9103 (t0) cc_final: 0.8598 (t0) REVERT: C 73 ILE cc_start: 0.8054 (mt) cc_final: 0.7814 (mp) REVERT: C 178 MET cc_start: 0.9629 (mtp) cc_final: 0.9158 (mtp) REVERT: C 258 LYS cc_start: 0.8984 (ptmt) cc_final: 0.8593 (pttp) REVERT: D 100 PHE cc_start: 0.8633 (t80) cc_final: 0.8130 (t80) REVERT: D 141 ILE cc_start: 0.8354 (mt) cc_final: 0.8013 (mm) REVERT: D 178 MET cc_start: 0.9409 (mtt) cc_final: 0.9064 (mtt) REVERT: D 184 ASN cc_start: 0.9074 (t0) cc_final: 0.8792 (t0) REVERT: D 243 TRP cc_start: 0.5750 (t60) cc_final: 0.5426 (t60) REVERT: J 258 LYS cc_start: 0.9168 (mttt) cc_final: 0.8751 (mtmm) REVERT: J 268 ILE cc_start: 0.9401 (pt) cc_final: 0.9082 (mp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1208 time to fit residues: 16.1304 Evaluate side-chains 72 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 0.0020 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.064652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.048254 restraints weight = 88537.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.049841 restraints weight = 47889.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050907 restraints weight = 32472.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051516 restraints weight = 25322.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.051828 restraints weight = 21730.624| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 12783 Z= 0.123 Angle : 0.625 7.808 17719 Z= 0.346 Chirality : 0.048 0.209 1929 Planarity : 0.004 0.045 1900 Dihedral : 24.765 80.642 2576 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -1.24 (0.23), residues: 1254 helix: 0.84 (0.23), residues: 482 sheet: -1.85 (0.29), residues: 290 loop : -1.80 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 107 TYR 0.032 0.001 TYR D 83 PHE 0.027 0.001 PHE A 100 TRP 0.052 0.001 TRP D 108 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (12783) covalent geometry : angle 0.62516 / 0.35 (17719) hydrogen bonds : bond 0.04250 / 2.81 ( 610) hydrogen bonds : angle 4.71927 / 3.32 ( 1652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.39 seconds wall clock time: 38 minutes 50.83 seconds (2330.83 seconds total)