Starting phenix.real_space_refine on Wed Jul 30 12:06:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vdk_21151/07_2025/6vdk_21151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vdk_21151/07_2025/6vdk_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_21151/07_2025/6vdk_21151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vdk_21151/07_2025/6vdk_21151.map" model { file = "/net/cci-nas-00/data/ceres_data/6vdk_21151/07_2025/6vdk_21151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vdk_21151/07_2025/6vdk_21151.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.57, per 1000 atoms: 0.70 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: 3.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.38 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: 3.91 Time building geometry restraints manager: 3.69 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: 0.000 Normalize map: mean=0, sd=1: 16.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.720 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP C 108 HIS 0.011 0.002 HIS A 183 PHE 0.016 0.002 PHE B 185 TYR 0.015 0.002 TYR A 83 ARG 0.006 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.15777 ( 610) hydrogen bonds : angle 6.92843 ( 1652) covalent geometry : bond 0.00801 (12783) covalent geometry : angle 0.97159 (17719) *********************** 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 : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9510 (mtp) cc_final: 0.9026 (mtp) REVERT: B 178 MET cc_start: 0.9498 (mtt) cc_final: 0.9124 (mtt) REVERT: B 184 ASN cc_start: 0.8938 (t0) cc_final: 0.8386 (t0) REVERT: C 178 MET cc_start: 0.9606 (mtp) cc_final: 0.9034 (mtp) 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: 0.9117 (mtt) REVERT: D 184 ASN cc_start: 0.9064 (t0) cc_final: 0.8636 (t0) REVERT: D 243 TRP cc_start: 0.5367 (t60) cc_final: 0.4936 (t60) REVERT: I 229 ASP cc_start: 0.8658 (t70) cc_final: 0.8454 (t70) REVERT: P 226 TYR cc_start: 0.7426 (m-80) cc_final: 0.7035 (m-80) REVERT: P 231 ARG cc_start: 0.7668 (ttt90) cc_final: 0.7287 (ttp80) outliers start: 7 outliers final: 0 residues processed: 132 average time/residue: 0.3173 time to fit residues: 56.0971 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 : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 0.0370 chunk 55 optimal weight: 0.0060 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9878 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 252 GLN B 183 HIS C 9 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 53 GLN C 183 HIS I 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.063603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.047732 restraints weight = 89160.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.049169 restraints weight = 49034.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.050205 restraints weight = 33440.922| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12783 Z= 0.171 Angle : 0.657 7.562 17719 Z= 0.382 Chirality : 0.048 0.234 1929 Planarity : 0.005 0.074 1900 Dihedral : 25.348 86.526 2576 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.19 % Allowed : 4.76 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1254 helix: -0.84 (0.21), residues: 471 sheet: -2.39 (0.28), residues: 286 loop : -2.23 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 19 HIS 0.006 0.001 HIS D 183 PHE 0.016 0.002 PHE C 100 TYR 0.021 0.001 TYR D 226 ARG 0.006 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.05842 ( 610) hydrogen bonds : angle 5.46663 ( 1652) covalent geometry : bond 0.00369 (12783) covalent geometry : angle 0.65679 (17719) *********************** 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 105 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9545 (mtp) cc_final: 0.9139 (mtp) REVERT: A 184 ASN cc_start: 0.8997 (m-40) cc_final: 0.8661 (t0) REVERT: B 22 MET cc_start: 0.7678 (mtm) cc_final: 0.7026 (mmt) REVERT: B 184 ASN cc_start: 0.9151 (t0) cc_final: 0.8558 (t0) REVERT: C 178 MET cc_start: 0.9670 (mtp) cc_final: 0.9162 (mtp) REVERT: D 22 MET cc_start: 0.7537 (mtm) cc_final: 0.7174 (mtm) REVERT: D 100 PHE cc_start: 0.8684 (t80) cc_final: 0.8184 (t80) REVERT: D 141 ILE cc_start: 0.8516 (mt) cc_final: 0.8206 (mm) REVERT: D 184 ASN cc_start: 0.9124 (t0) cc_final: 0.8745 (t0) REVERT: D 243 TRP cc_start: 0.5271 (t60) cc_final: 0.4935 (t60) REVERT: I 221 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: J 229 ASP cc_start: 0.8690 (t0) cc_final: 0.8481 (t70) REVERT: M 226 TYR cc_start: 0.7751 (m-80) cc_final: 0.6995 (m-80) REVERT: P 230 SER cc_start: 0.8076 (m) cc_final: 0.7632 (p) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.2925 time to fit residues: 42.7266 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 : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN B 18 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.061179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045018 restraints weight = 92058.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046486 restraints weight = 51852.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047475 restraints weight = 35616.049| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12783 Z= 0.239 Angle : 0.684 8.646 17719 Z= 0.395 Chirality : 0.048 0.221 1929 Planarity : 0.005 0.053 1900 Dihedral : 25.288 88.917 2576 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.22), residues: 1254 helix: -0.34 (0.21), residues: 474 sheet: -2.45 (0.28), residues: 277 loop : -2.15 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 61 HIS 0.006 0.002 HIS D 183 PHE 0.013 0.002 PHE C 26 TYR 0.019 0.002 TYR D 226 ARG 0.005 0.001 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.06744 ( 610) hydrogen bonds : angle 5.43216 ( 1652) covalent geometry : bond 0.00506 (12783) covalent geometry : angle 0.68386 (17719) *********************** 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 87 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9598 (mtp) cc_final: 0.9196 (mtp) REVERT: A 182 ILE cc_start: 0.9786 (mt) cc_final: 0.9540 (mt) REVERT: A 184 ASN cc_start: 0.9088 (m-40) cc_final: 0.8779 (t0) REVERT: B 22 MET cc_start: 0.7900 (mtm) cc_final: 0.7411 (mmt) REVERT: B 184 ASN cc_start: 0.9072 (t0) cc_final: 0.8494 (t0) REVERT: C 62 GLN cc_start: 0.9125 (mt0) cc_final: 0.8903 (mt0) REVERT: C 73 ILE cc_start: 0.8086 (mt) cc_final: 0.7826 (mp) REVERT: C 178 MET cc_start: 0.9682 (mtp) cc_final: 0.9196 (mtp) REVERT: C 182 ILE cc_start: 0.9772 (mt) cc_final: 0.9571 (mt) REVERT: C 184 ASN cc_start: 0.9461 (m-40) cc_final: 0.8948 (t0) REVERT: D 100 PHE cc_start: 0.8626 (t80) cc_final: 0.8295 (t80) REVERT: D 141 ILE cc_start: 0.8582 (mt) cc_final: 0.8261 (mm) REVERT: D 184 ASN cc_start: 0.9117 (t0) cc_final: 0.8786 (t0) REVERT: D 243 TRP cc_start: 0.5356 (t60) cc_final: 0.5003 (t60) REVERT: J 229 ASP cc_start: 0.8764 (t0) cc_final: 0.8479 (t70) REVERT: P 226 TYR cc_start: 0.7957 (m-80) cc_final: 0.7720 (m-80) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.2557 time to fit residues: 32.7836 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 : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 144 ASN A 146 GLN A 252 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.062971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046782 restraints weight = 89582.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.048290 restraints weight = 49818.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.049331 restraints weight = 34067.859| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12783 Z= 0.154 Angle : 0.604 7.917 17719 Z= 0.351 Chirality : 0.046 0.185 1929 Planarity : 0.004 0.052 1900 Dihedral : 25.175 87.569 2576 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.22), residues: 1254 helix: 0.21 (0.22), residues: 476 sheet: -2.32 (0.28), residues: 282 loop : -2.06 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.006 0.001 HIS D 183 PHE 0.012 0.001 PHE C 100 TYR 0.016 0.001 TYR D 226 ARG 0.011 0.000 ARG M 269 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 610) hydrogen bonds : angle 5.07892 ( 1652) covalent geometry : bond 0.00329 (12783) covalent geometry : angle 0.60447 (17719) *********************** 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 88 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9589 (mtp) cc_final: 0.9170 (mtp) REVERT: A 182 ILE cc_start: 0.9771 (mt) cc_final: 0.9537 (mt) REVERT: A 184 ASN cc_start: 0.9069 (m-40) cc_final: 0.8653 (t0) REVERT: A 216 GLN cc_start: 0.9151 (tt0) cc_final: 0.8842 (tp40) REVERT: B 22 MET cc_start: 0.7793 (mtm) cc_final: 0.7458 (mmt) REVERT: B 178 MET cc_start: 0.9425 (mtt) cc_final: 0.9132 (mtt) REVERT: B 184 ASN cc_start: 0.9044 (t0) cc_final: 0.8556 (t0) REVERT: C 73 ILE cc_start: 0.8054 (mt) cc_final: 0.7794 (mp) REVERT: C 178 MET cc_start: 0.9669 (mtp) cc_final: 0.9129 (mtp) REVERT: C 184 ASN cc_start: 0.9447 (m-40) cc_final: 0.8876 (t0) REVERT: D 100 PHE cc_start: 0.8575 (t80) cc_final: 0.8220 (t80) REVERT: D 141 ILE cc_start: 0.8522 (mt) cc_final: 0.8183 (mm) REVERT: D 184 ASN cc_start: 0.9106 (t0) cc_final: 0.8758 (t0) REVERT: D 243 TRP cc_start: 0.5384 (t60) cc_final: 0.5070 (t60) REVERT: J 229 ASP cc_start: 0.8766 (t0) cc_final: 0.8488 (t70) REVERT: P 226 TYR cc_start: 0.7915 (m-80) cc_final: 0.7641 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2461 time to fit residues: 31.6143 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 : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.061328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045244 restraints weight = 91321.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.046665 restraints weight = 50932.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.047671 restraints weight = 35107.355| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12783 Z= 0.216 Angle : 0.640 8.481 17719 Z= 0.369 Chirality : 0.046 0.190 1929 Planarity : 0.005 0.089 1900 Dihedral : 25.130 85.655 2576 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1254 helix: 0.25 (0.21), residues: 489 sheet: -2.23 (0.30), residues: 257 loop : -2.01 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 19 HIS 0.007 0.002 HIS B 67 PHE 0.012 0.001 PHE C 26 TYR 0.017 0.001 TYR D 226 ARG 0.011 0.001 ARG D 228 Details of bonding type rmsd hydrogen bonds : bond 0.05950 ( 610) hydrogen bonds : angle 5.16465 ( 1652) covalent geometry : bond 0.00458 (12783) covalent geometry : angle 0.64009 (17719) *********************** 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 85 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9608 (mtp) cc_final: 0.8688 (mtm) REVERT: A 182 ILE cc_start: 0.9765 (mt) cc_final: 0.9511 (mt) REVERT: A 184 ASN cc_start: 0.9037 (m-40) cc_final: 0.8775 (t0) REVERT: A 216 GLN cc_start: 0.9182 (tt0) cc_final: 0.8888 (tp40) REVERT: B 184 ASN cc_start: 0.9043 (t0) cc_final: 0.8551 (t0) REVERT: C 73 ILE cc_start: 0.8074 (mt) cc_final: 0.7819 (mp) REVERT: C 178 MET cc_start: 0.9672 (mtp) cc_final: 0.9157 (mtp) REVERT: C 182 ILE cc_start: 0.9769 (mt) cc_final: 0.9554 (mt) REVERT: C 184 ASN cc_start: 0.9487 (m-40) cc_final: 0.8910 (t0) REVERT: D 100 PHE cc_start: 0.8615 (t80) cc_final: 0.8206 (t80) REVERT: D 107 ARG cc_start: 0.8580 (mmp80) cc_final: 0.8361 (mmp80) REVERT: D 141 ILE cc_start: 0.8411 (mt) cc_final: 0.8089 (mm) REVERT: D 184 ASN cc_start: 0.9111 (t0) cc_final: 0.8761 (t0) REVERT: J 229 ASP cc_start: 0.8824 (t0) cc_final: 0.8521 (t70) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2409 time to fit residues: 30.4801 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 : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 10 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN B 67 HIS ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.062112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046041 restraints weight = 89725.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.047490 restraints weight = 50038.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048514 restraints weight = 34230.422| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12783 Z= 0.175 Angle : 0.616 8.296 17719 Z= 0.354 Chirality : 0.046 0.173 1929 Planarity : 0.004 0.051 1900 Dihedral : 25.084 84.349 2576 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.23), residues: 1254 helix: 0.39 (0.21), residues: 489 sheet: -2.29 (0.29), residues: 272 loop : -1.97 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 243 HIS 0.008 0.001 HIS B 67 PHE 0.032 0.001 PHE A 100 TYR 0.016 0.001 TYR D 226 ARG 0.005 0.000 ARG D 228 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 610) hydrogen bonds : angle 5.04071 ( 1652) covalent geometry : bond 0.00377 (12783) covalent geometry : angle 0.61597 (17719) *********************** 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 : 1.186 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: 0.9605 (mtp) cc_final: 0.8646 (mtm) REVERT: A 182 ILE cc_start: 0.9777 (mt) cc_final: 0.9517 (mt) REVERT: A 184 ASN cc_start: 0.9075 (m-40) cc_final: 0.8791 (t0) REVERT: A 216 GLN cc_start: 0.9201 (tt0) cc_final: 0.8918 (tp40) REVERT: B 22 MET cc_start: 0.7961 (mtm) cc_final: 0.7368 (mtm) REVERT: B 178 MET cc_start: 0.9444 (mtt) cc_final: 0.9135 (mtt) REVERT: B 184 ASN cc_start: 0.9051 (t0) cc_final: 0.8555 (t0) REVERT: C 73 ILE cc_start: 0.8050 (mt) cc_final: 0.7793 (mp) REVERT: C 178 MET cc_start: 0.9682 (mtp) cc_final: 0.9183 (mtp) REVERT: C 184 ASN cc_start: 0.9482 (m-40) cc_final: 0.8838 (t0) REVERT: D 100 PHE cc_start: 0.8657 (t80) cc_final: 0.8284 (t80) REVERT: D 141 ILE cc_start: 0.8360 (mt) cc_final: 0.8021 (mm) REVERT: D 184 ASN cc_start: 0.9104 (t0) cc_final: 0.8787 (t0) REVERT: D 243 TRP cc_start: 0.4317 (t60) cc_final: 0.3977 (t60) REVERT: D 255 SER cc_start: 0.7948 (p) cc_final: 0.7713 (m) REVERT: J 229 ASP cc_start: 0.8837 (t0) cc_final: 0.8537 (t70) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2125 time to fit residues: 28.1804 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 : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 31 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 252 GLN ** C 27 ASN ** 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 = 0.3687 r_free = 0.3687 target = 0.064278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.047799 restraints weight = 88023.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.049412 restraints weight = 48701.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050525 restraints weight = 33046.113| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12783 Z= 0.132 Angle : 0.587 7.522 17719 Z= 0.337 Chirality : 0.046 0.169 1929 Planarity : 0.004 0.046 1900 Dihedral : 24.961 88.574 2576 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1254 helix: 0.63 (0.22), residues: 482 sheet: -2.15 (0.28), residues: 295 loop : -1.89 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 243 HIS 0.006 0.001 HIS D 183 PHE 0.014 0.001 PHE C 100 TYR 0.015 0.001 TYR D 226 ARG 0.007 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 610) hydrogen bonds : angle 4.79202 ( 1652) covalent geometry : bond 0.00284 (12783) covalent geometry : angle 0.58714 (17719) *********************** 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 99 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9615 (mtp) cc_final: 0.8608 (mtm) REVERT: A 182 ILE cc_start: 0.9785 (mt) cc_final: 0.9553 (mt) REVERT: A 184 ASN cc_start: 0.8988 (m-40) cc_final: 0.8708 (t0) REVERT: A 216 GLN cc_start: 0.9195 (tt0) cc_final: 0.8938 (tp40) REVERT: B 184 ASN cc_start: 0.9152 (t0) cc_final: 0.8614 (t0) REVERT: C 73 ILE cc_start: 0.8025 (mt) cc_final: 0.7822 (mp) REVERT: C 178 MET cc_start: 0.9689 (mtp) cc_final: 0.9176 (mtp) REVERT: C 184 ASN cc_start: 0.9461 (m-40) cc_final: 0.8904 (t0) REVERT: D 100 PHE cc_start: 0.8602 (t80) cc_final: 0.8157 (t80) REVERT: D 107 ARG cc_start: 0.8468 (mmp80) cc_final: 0.8240 (mmp80) REVERT: D 141 ILE cc_start: 0.8425 (mt) cc_final: 0.8084 (mm) REVERT: D 178 MET cc_start: 0.9471 (mtt) cc_final: 0.9201 (mtt) REVERT: D 184 ASN cc_start: 0.9135 (t0) cc_final: 0.8742 (t0) REVERT: D 243 TRP cc_start: 0.4781 (t60) cc_final: 0.4149 (t60) REVERT: D 255 SER cc_start: 0.7995 (p) cc_final: 0.7790 (m) REVERT: J 229 ASP cc_start: 0.8800 (t0) cc_final: 0.8486 (t70) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2204 time to fit residues: 33.3089 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 : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.0030 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 121 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** 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 = 0.3707 r_free = 0.3707 target = 0.065072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.048447 restraints weight = 88863.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.050050 restraints weight = 48548.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.051207 restraints weight = 32849.170| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3185 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= 0.127 Angle : 0.587 9.249 17719 Z= 0.330 Chirality : 0.045 0.148 1929 Planarity : 0.004 0.043 1900 Dihedral : 24.811 84.912 2576 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1254 helix: 0.80 (0.22), residues: 483 sheet: -2.02 (0.28), residues: 301 loop : -1.80 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 108 HIS 0.004 0.001 HIS D 183 PHE 0.020 0.001 PHE C 100 TYR 0.014 0.001 TYR D 226 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 610) hydrogen bonds : angle 4.64306 ( 1652) covalent geometry : bond 0.00272 (12783) covalent geometry : angle 0.58673 (17719) *********************** 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 105 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.246 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: 0.9594 (mtp) cc_final: 0.8468 (mtm) REVERT: A 182 ILE cc_start: 0.9766 (mt) cc_final: 0.9515 (mt) REVERT: A 216 GLN cc_start: 0.9188 (tt0) cc_final: 0.8952 (tp40) REVERT: B 178 MET cc_start: 0.9440 (mtt) cc_final: 0.9040 (mtt) REVERT: B 184 ASN cc_start: 0.9098 (t0) cc_final: 0.8597 (t0) REVERT: C 178 MET cc_start: 0.9652 (mtp) cc_final: 0.9121 (mtp) REVERT: C 184 ASN cc_start: 0.9390 (m-40) cc_final: 0.8865 (t0) REVERT: C 258 LYS cc_start: 0.9010 (ptmt) cc_final: 0.8592 (pttp) REVERT: D 100 PHE cc_start: 0.8554 (t80) cc_final: 0.8095 (t80) REVERT: D 141 ILE cc_start: 0.8406 (mt) cc_final: 0.8064 (mm) REVERT: D 178 MET cc_start: 0.9431 (mtt) cc_final: 0.9069 (mtt) REVERT: D 184 ASN cc_start: 0.9133 (t0) cc_final: 0.8835 (t0) REVERT: D 243 TRP cc_start: 0.4579 (t60) cc_final: 0.4091 (t60) REVERT: D 255 SER cc_start: 0.7970 (p) cc_final: 0.7763 (m) REVERT: J 229 ASP cc_start: 0.8800 (t0) cc_final: 0.8478 (t70) REVERT: J 251 ILE cc_start: 0.8877 (pt) cc_final: 0.8564 (tp) REVERT: J 258 LYS cc_start: 0.9139 (mttt) cc_final: 0.8619 (mtmm) REVERT: M 226 TYR cc_start: 0.7370 (m-80) cc_final: 0.6874 (m-80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2391 time to fit residues: 37.1874 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 : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 130 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN D 67 HIS ** D 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.064169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.047399 restraints weight = 86024.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.048980 restraints weight = 47356.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.050067 restraints weight = 32078.894| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12783 Z= 0.131 Angle : 0.585 7.285 17719 Z= 0.332 Chirality : 0.045 0.194 1929 Planarity : 0.004 0.045 1900 Dihedral : 24.735 83.939 2576 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1254 helix: 0.91 (0.23), residues: 483 sheet: -1.92 (0.28), residues: 290 loop : -1.76 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 108 HIS 0.004 0.001 HIS A 12 PHE 0.011 0.001 PHE A 100 TYR 0.020 0.001 TYR D 83 ARG 0.007 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 610) hydrogen bonds : angle 4.62105 ( 1652) covalent geometry : bond 0.00285 (12783) covalent geometry : angle 0.58488 (17719) *********************** 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 99 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9581 (mtp) cc_final: 0.8473 (mtm) REVERT: A 182 ILE cc_start: 0.9759 (mt) cc_final: 0.9509 (mt) REVERT: B 178 MET cc_start: 0.9420 (mtt) cc_final: 0.8992 (mtt) REVERT: B 184 ASN cc_start: 0.9089 (t0) cc_final: 0.8621 (t0) REVERT: C 73 ILE cc_start: 0.8129 (mt) cc_final: 0.7925 (mp) REVERT: C 178 MET cc_start: 0.9585 (mtp) cc_final: 0.9096 (mtp) REVERT: C 184 ASN cc_start: 0.9443 (m-40) cc_final: 0.8822 (t0) REVERT: C 258 LYS cc_start: 0.9065 (ptmt) cc_final: 0.8642 (pttp) REVERT: D 100 PHE cc_start: 0.8601 (t80) cc_final: 0.8064 (t80) REVERT: D 104 LEU cc_start: 0.9433 (mt) cc_final: 0.9193 (mt) REVERT: D 141 ILE cc_start: 0.8399 (mt) cc_final: 0.8066 (mm) REVERT: D 178 MET cc_start: 0.9413 (mtt) cc_final: 0.9044 (mtt) REVERT: D 184 ASN cc_start: 0.9136 (t0) cc_final: 0.8883 (t0) REVERT: D 243 TRP cc_start: 0.4870 (t60) cc_final: 0.4382 (t60) REVERT: D 255 SER cc_start: 0.8011 (p) cc_final: 0.7800 (m) REVERT: J 229 ASP cc_start: 0.8804 (t0) cc_final: 0.8469 (t70) REVERT: J 251 ILE cc_start: 0.8783 (pt) cc_final: 0.8485 (tp) REVERT: J 254 ASN cc_start: 0.8979 (m-40) cc_final: 0.8325 (p0) REVERT: J 258 LYS cc_start: 0.9152 (mttt) cc_final: 0.8678 (mtmm) REVERT: J 268 ILE cc_start: 0.9413 (pt) cc_final: 0.9114 (mp) REVERT: M 226 TYR cc_start: 0.7383 (m-80) cc_final: 0.6920 (m-80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2419 time to fit residues: 35.4138 Evaluate side-chains 79 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS ** 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 = 0.3687 r_free = 0.3687 target = 0.064395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.047887 restraints weight = 87966.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.049503 restraints weight = 48556.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.050583 restraints weight = 32950.098| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12783 Z= 0.147 Angle : 0.592 7.734 17719 Z= 0.336 Chirality : 0.044 0.181 1929 Planarity : 0.004 0.043 1900 Dihedral : 24.701 88.531 2576 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1254 helix: 1.03 (0.23), residues: 483 sheet: -1.89 (0.28), residues: 294 loop : -1.72 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 108 HIS 0.003 0.001 HIS A 183 PHE 0.019 0.001 PHE A 100 TYR 0.019 0.001 TYR D 83 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 610) hydrogen bonds : angle 4.67264 ( 1652) covalent geometry : bond 0.00318 (12783) covalent geometry : angle 0.59238 (17719) ********************** 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 96 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9613 (mtp) cc_final: 0.8523 (mtm) REVERT: A 182 ILE cc_start: 0.9770 (mt) cc_final: 0.9559 (mt) REVERT: B 184 ASN cc_start: 0.9095 (t0) cc_final: 0.8619 (t0) REVERT: C 73 ILE cc_start: 0.8078 (mt) cc_final: 0.7818 (mp) REVERT: C 178 MET cc_start: 0.9608 (mtp) cc_final: 0.9132 (mtp) REVERT: C 184 ASN cc_start: 0.9497 (m-40) cc_final: 0.8781 (t0) REVERT: C 258 LYS cc_start: 0.9078 (ptmt) cc_final: 0.8685 (pttp) REVERT: D 100 PHE cc_start: 0.8637 (t80) cc_final: 0.8177 (t80) REVERT: D 104 LEU cc_start: 0.9422 (mt) cc_final: 0.9221 (mt) REVERT: D 141 ILE cc_start: 0.8408 (mt) cc_final: 0.8077 (mm) REVERT: D 184 ASN cc_start: 0.9149 (t0) cc_final: 0.8867 (t0) REVERT: D 243 TRP cc_start: 0.5085 (t60) cc_final: 0.4589 (t60) REVERT: D 255 SER cc_start: 0.7982 (p) cc_final: 0.7759 (m) REVERT: J 229 ASP cc_start: 0.8841 (t0) cc_final: 0.8479 (t70) REVERT: J 251 ILE cc_start: 0.8793 (pt) cc_final: 0.8502 (tp) REVERT: J 258 LYS cc_start: 0.9151 (mttt) cc_final: 0.8669 (mtmm) REVERT: J 268 ILE cc_start: 0.9410 (pt) cc_final: 0.9118 (mp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2402 time to fit residues: 34.2752 Evaluate side-chains 75 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 4.9990 chunk 55 optimal weight: 0.0270 chunk 9 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 96 optimal weight: 0.0030 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 25 optimal weight: 0.0470 chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 0.0060 chunk 68 optimal weight: 0.8980 overall best weight: 0.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN D 78 HIS D 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.066777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.050112 restraints weight = 86211.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051817 restraints weight = 46845.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052982 restraints weight = 31538.226| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12783 Z= 0.123 Angle : 0.583 6.610 17719 Z= 0.327 Chirality : 0.045 0.158 1929 Planarity : 0.004 0.045 1900 Dihedral : 24.567 77.660 2576 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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 : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1254 helix: 1.11 (0.23), residues: 483 sheet: -1.63 (0.28), residues: 290 loop : -1.76 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 108 HIS 0.005 0.001 HIS A 51 PHE 0.008 0.001 PHE C 100 TYR 0.018 0.001 TYR D 83 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 610) hydrogen bonds : angle 4.49006 ( 1652) covalent geometry : bond 0.00266 (12783) covalent geometry : angle 0.58347 (17719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.43 seconds wall clock time: 75 minutes 39.65 seconds (4539.65 seconds total)