Starting phenix.real_space_refine on Wed Mar 4 12:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kls_0716/03_2026/6kls_0716.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kls_0716/03_2026/6kls_0716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kls_0716/03_2026/6kls_0716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kls_0716/03_2026/6kls_0716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kls_0716/03_2026/6kls_0716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kls_0716/03_2026/6kls_0716.map" } resolution = 3.3 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= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 3 5.49 5 S 56 5.16 5 C 8872 2.51 5 N 1968 2.21 5 O 2102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13011 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 118} Chain breaks: 2 Chain: "B" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3226 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "C" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1917 Classifications: {'peptide': 236} Link IDs: {'CIS': 6, 'PTRANS': 15, 'TRANS': 214} Chain: "D" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Link IDs: {'CIS': 2, 'PTRANS': 13, 'TRANS': 118} Chain breaks: 2 Chain: "E" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3226 Classifications: {'peptide': 395} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Chain: "F" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1917 Classifications: {'peptide': 236} Link IDs: {'CIS': 6, 'PTRANS': 15, 'TRANS': 214} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 282 Unusual residues: {'DLX': 2, 'HEM': 2, 'PGV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'DLX': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 231 Unusual residues: {'DLX': 2, 'HEM': 2, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'DLX': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 626 SG CYS A 111 29.763 32.691 19.945 1.00 1.00 S ATOM 748 SG CYS A 135 31.243 32.795 16.781 1.00 1.00 S ATOM 6781 SG CYS D 111 73.123 70.219 19.957 1.00 1.00 S ATOM 6903 SG CYS D 135 71.643 70.116 16.792 1.00 1.00 S Time building chain proxies: 2.54, per 1000 atoms: 0.20 Number of scatterers: 13011 At special positions: 0 Unit cell: (103.95, 103.95, 105, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 56 16.00 P 3 15.00 O 2102 8.00 N 1968 7.00 C 8872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 116 " - pdb=" SG CYS D 137 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 598.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 501 " pdb="FE2 FES A 501 " - pdb=" ND1 HIS A 138 " pdb="FE2 FES A 501 " - pdb=" NE2 HIS A 113 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 111 " pdb="FE1 FES A 501 " - pdb=" SG CYS A 135 " pdb=" FES D 501 " pdb="FE2 FES D 501 " - pdb=" ND1 HIS D 138 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 111 " pdb="FE2 FES D 501 " - pdb=" NE2 HIS D 113 " pdb="FE1 FES D 501 " - pdb=" SG CYS D 135 " Number of angles added : 6 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2836 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 54.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'B' and resid 8 through 16 removed outlier: 3.541A pdb=" N ARG B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 25 removed outlier: 3.621A pdb=" N THR B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.678A pdb=" N TYR B 38 " --> pdb=" O THR B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 39 through 59 removed outlier: 3.756A pdb=" N VAL B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 83 through 112 removed outlier: 3.507A pdb=" N HIS B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 140 removed outlier: 3.645A pdb=" N TRP B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.140A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 191 through 225 removed outlier: 4.730A pdb=" N TYR B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.871A pdb=" N TYR B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 272 removed outlier: 3.600A pdb=" N MET B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.834A pdb=" N VAL B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 344 through 365 removed outlier: 4.189A pdb=" N VAL B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.891A pdb=" N PHE B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.725A pdb=" N GLY B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.631A pdb=" N GLY C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 16 " --> pdb=" O PHE C 12 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.802A pdb=" N GLY C 55 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 70 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.503A pdb=" N ALA C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 161 through 166 removed outlier: 3.783A pdb=" N VAL C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 203 through 238 removed outlier: 3.678A pdb=" N THR C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 33 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'E' and resid 8 through 16 removed outlier: 3.541A pdb=" N ARG E 14 " --> pdb=" O TRP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 25 removed outlier: 3.620A pdb=" N THR E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 38 removed outlier: 3.677A pdb=" N TYR E 38 " --> pdb=" O THR E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 35 through 38' Processing helix chain 'E' and resid 39 through 59 removed outlier: 3.755A pdb=" N VAL E 57 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 83 through 112 removed outlier: 3.506A pdb=" N HIS E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 140 removed outlier: 3.645A pdb=" N TRP E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 159 removed outlier: 4.140A pdb=" N TRP E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 191 through 225 removed outlier: 4.729A pdb=" N TYR E 206 " --> pdb=" O HIS E 202 " (cutoff:3.500A) Proline residue: E 207 - end of helix Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.870A pdb=" N TYR E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 272 removed outlier: 3.600A pdb=" N MET E 259 " --> pdb=" O GLY E 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 300 through 307 removed outlier: 3.834A pdb=" N VAL E 306 " --> pdb=" O GLY E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 344 through 365 removed outlier: 4.190A pdb=" N VAL E 349 " --> pdb=" O PRO E 345 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 361 " --> pdb=" O SER E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 390 removed outlier: 3.891A pdb=" N PHE E 388 " --> pdb=" O VAL E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 removed outlier: 3.725A pdb=" N GLY E 400 " --> pdb=" O PHE E 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 25 removed outlier: 3.631A pdb=" N GLY F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.803A pdb=" N GLY F 55 " --> pdb=" O THR F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 70 Processing helix chain 'F' and resid 145 through 151 removed outlier: 3.504A pdb=" N ALA F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 159 Processing helix chain 'F' and resid 161 through 166 removed outlier: 3.784A pdb=" N VAL F 165 " --> pdb=" O ASN F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 Processing helix chain 'F' and resid 203 through 238 removed outlier: 3.678A pdb=" N THR F 209 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS F 235 " --> pdb=" O GLU F 231 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.734A pdb=" N ILE A 47 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 removed outlier: 3.838A pdb=" N GLN A 56 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 71 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 70 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 105 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.613A pdb=" N GLY A 140 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 104 removed outlier: 6.604A pdb=" N ARG C 113 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 47 through 48 removed outlier: 3.734A pdb=" N ILE D 47 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 60 removed outlier: 3.837A pdb=" N GLN D 56 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 71 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 70 " --> pdb=" O PHE D 105 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 105 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.613A pdb=" N GLY D 140 " --> pdb=" O CYS D 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 102 through 104 removed outlier: 6.605A pdb=" N ARG F 113 " --> pdb=" O VAL F 103 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 5244 1.39 - 1.60: 8066 1.60 - 1.81: 120 1.81 - 2.02: 2 2.02 - 2.24: 32 Bond restraints: 13464 Sorted by residual: bond pdb=" C30 DLX B 504 " pdb=" C31 DLX B 504 " ideal model delta sigma weight residual 1.335 1.658 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C30 DLX E 504 " pdb=" C31 DLX E 504 " ideal model delta sigma weight residual 1.335 1.658 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C30 DLX F 301 " pdb=" C31 DLX F 301 " ideal model delta sigma weight residual 1.335 1.656 -0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C30 DLX C 301 " pdb=" C31 DLX C 301 " ideal model delta sigma weight residual 1.335 1.655 -0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" C22 DLX E 504 " pdb=" C23 DLX E 504 " ideal model delta sigma weight residual 1.335 1.597 -0.262 2.00e-02 2.50e+03 1.71e+02 ... (remaining 13459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 18035 3.48 - 6.96: 201 6.96 - 10.44: 49 10.44 - 13.91: 32 13.91 - 17.39: 25 Bond angle restraints: 18342 Sorted by residual: angle pdb=" S1 FES A 501 " pdb="FE2 FES A 501 " pdb=" S2 FES A 501 " ideal model delta sigma weight residual 104.33 89.99 14.34 1.14e+00 7.69e-01 1.58e+02 angle pdb=" S1 FES D 501 " pdb="FE2 FES D 501 " pdb=" S2 FES D 501 " ideal model delta sigma weight residual 104.33 90.05 14.28 1.14e+00 7.69e-01 1.57e+02 angle pdb=" S1 FES A 501 " pdb="FE1 FES A 501 " pdb=" S2 FES A 501 " ideal model delta sigma weight residual 104.33 89.99 14.34 1.20e+00 6.94e-01 1.43e+02 angle pdb=" S1 FES D 501 " pdb="FE1 FES D 501 " pdb=" S2 FES D 501 " ideal model delta sigma weight residual 104.33 90.04 14.29 1.20e+00 6.94e-01 1.42e+02 angle pdb="FE1 FES D 501 " pdb=" S2 FES D 501 " pdb="FE2 FES D 501 " ideal model delta sigma weight residual 75.66 88.44 -12.78 1.14e+00 7.69e-01 1.26e+02 ... (remaining 18337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 7423 34.29 - 68.58: 241 68.58 - 102.87: 29 102.87 - 137.15: 10 137.15 - 171.44: 6 Dihedral angle restraints: 7709 sinusoidal: 3271 harmonic: 4438 Sorted by residual: dihedral pdb=" CA GLY D 151 " pdb=" C GLY D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLY A 151 " pdb=" C GLY A 151 " pdb=" N PRO A 152 " pdb=" CA PRO A 152 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PRO F 140 " pdb=" C PRO F 140 " pdb=" N PRO F 141 " pdb=" CA PRO F 141 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 7706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1796 0.093 - 0.187: 105 0.187 - 0.280: 11 0.280 - 0.373: 0 0.373 - 0.467: 2 Chirality restraints: 1914 Sorted by residual: chirality pdb=" CA LEU C 160 " pdb=" N LEU C 160 " pdb=" C LEU C 160 " pdb=" CB LEU C 160 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA LEU F 160 " pdb=" N LEU F 160 " pdb=" C LEU F 160 " pdb=" CB LEU F 160 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C05 PGV B 506 " pdb=" C04 PGV B 506 " pdb=" C06 PGV B 506 " pdb=" O05 PGV B 506 " both_signs ideal model delta sigma weight residual False 2.29 2.55 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1911 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 DLX C 301 " 0.456 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" C26 DLX C 301 " -0.469 2.00e-02 2.50e+03 pdb=" C27 DLX C 301 " -0.445 2.00e-02 2.50e+03 pdb=" C28 DLX C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C44 DLX C 301 " 0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 DLX F 301 " -0.456 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" C26 DLX F 301 " 0.469 2.00e-02 2.50e+03 pdb=" C27 DLX F 301 " 0.445 2.00e-02 2.50e+03 pdb=" C28 DLX F 301 " -0.006 2.00e-02 2.50e+03 pdb=" C44 DLX F 301 " -0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 DLX B 504 " 0.298 2.00e-02 2.50e+03 3.21e-01 1.29e+03 pdb=" C26 DLX B 504 " -0.591 2.00e-02 2.50e+03 pdb=" C27 DLX B 504 " 0.278 2.00e-02 2.50e+03 pdb=" C28 DLX B 504 " 0.015 2.00e-02 2.50e+03 pdb=" C44 DLX B 504 " -0.001 2.00e-02 2.50e+03 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 98 2.57 - 3.16: 10642 3.16 - 3.74: 19838 3.74 - 4.32: 29420 4.32 - 4.90: 47153 Nonbonded interactions: 107151 Sorted by model distance: nonbonded pdb=" O GLY C 168 " pdb=" CD2 HIS D 138 " model vdw 1.992 3.260 nonbonded pdb=" O PHE B 335 " pdb=" OG SER B 395 " model vdw 2.060 3.040 nonbonded pdb=" O PHE E 335 " pdb=" OG SER E 395 " model vdw 2.060 3.040 nonbonded pdb=" CD2 HIS A 138 " pdb=" O GLY F 168 " model vdw 2.135 3.260 nonbonded pdb=" OE1 GLU A 34 " pdb=" OG SER A 36 " model vdw 2.210 3.040 ... (remaining 107146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 7 through 505) selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.010 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.018 0.517 13486 Z= 0.946 Angle : 1.247 28.343 18352 Z= 0.569 Chirality : 0.051 0.467 1914 Planarity : 0.030 0.408 2207 Dihedral : 18.651 171.443 4867 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.66 % Favored : 89.21 % Rotamer: Outliers : 0.69 % Allowed : 5.44 % Favored : 93.87 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -3.67 (0.19), residues: 1510 helix: -1.53 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -3.57 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 308 TYR 0.013 0.001 TYR E 234 PHE 0.020 0.002 PHE F 25 TRP 0.007 0.001 TRP C 92 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.01411 (13464) covalent geometry : angle 1.21864 (18342) SS BOND : bond 0.00027 ( 2) SS BOND : angle 0.37797 ( 4) hydrogen bonds : bond 0.15972 ( 554) hydrogen bonds : angle 6.54676 ( 1626) metal coordination : bond 0.08243 ( 8) metal coordination : angle 14.60852 ( 6) Misc. bond : bond 0.37145 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7669 (t0) cc_final: 0.7435 (t0) REVERT: B 18 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6514 (mmp-170) REVERT: B 250 MET cc_start: 0.8260 (tpp) cc_final: 0.7966 (tpp) REVERT: B 259 MET cc_start: 0.8690 (mmt) cc_final: 0.8081 (mmt) REVERT: B 320 PHE cc_start: 0.7950 (t80) cc_final: 0.7554 (t80) REVERT: B 350 MET cc_start: 0.8999 (mmm) cc_final: 0.8784 (mmp) REVERT: E 12 ASP cc_start: 0.7690 (t0) cc_final: 0.7467 (t0) REVERT: E 18 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6452 (mmp-170) REVERT: E 250 MET cc_start: 0.8231 (tpp) cc_final: 0.7955 (tpp) REVERT: E 259 MET cc_start: 0.8690 (mmt) cc_final: 0.8079 (mmt) REVERT: E 320 PHE cc_start: 0.7969 (t80) cc_final: 0.7546 (t80) outliers start: 9 outliers final: 2 residues processed: 216 average time/residue: 0.1281 time to fit residues: 38.7368 Evaluate side-chains 157 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 147 GLN B 373 ASN C 176 ASN C 198 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN E 147 GLN E 373 ASN F 176 ASN F 182 GLN F 198 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.152576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.118259 restraints weight = 15825.805| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.58 r_work: 0.2928 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 13486 Z= 0.150 Angle : 0.775 18.737 18352 Z= 0.349 Chirality : 0.045 0.159 1914 Planarity : 0.005 0.068 2207 Dihedral : 17.485 173.693 1991 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.20 % Favored : 89.67 % Rotamer: Outliers : 2.07 % Allowed : 10.18 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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 (0.21), residues: 1510 helix: -0.29 (0.19), residues: 798 sheet: None (None), residues: 0 loop : -3.23 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.010 0.001 TYR E 249 PHE 0.020 0.002 PHE E 320 TRP 0.010 0.001 TRP E 183 HIS 0.009 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00357 (13464) covalent geometry : angle 0.75505 (18342) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.24419 ( 4) hydrogen bonds : bond 0.04559 ( 554) hydrogen bonds : angle 4.71896 ( 1626) metal coordination : bond 0.02154 ( 8) metal coordination : angle 9.81539 ( 6) Misc. bond : bond 0.07197 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8381 (t0) cc_final: 0.7934 (t0) REVERT: B 18 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6021 (mmp-170) REVERT: B 99 MET cc_start: 0.9121 (mmm) cc_final: 0.8776 (mmm) REVERT: B 259 MET cc_start: 0.9133 (mmt) cc_final: 0.8922 (mmm) REVERT: B 350 MET cc_start: 0.9396 (mmm) cc_final: 0.9191 (tpp) REVERT: C 211 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8806 (ttp) REVERT: E 12 ASP cc_start: 0.8410 (t0) cc_final: 0.7962 (t0) REVERT: E 18 ARG cc_start: 0.6956 (mtp180) cc_final: 0.5973 (mmp-170) REVERT: E 99 MET cc_start: 0.9119 (mmm) cc_final: 0.8775 (mmm) REVERT: E 297 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7884 (mm-30) REVERT: E 320 PHE cc_start: 0.7778 (t80) cc_final: 0.7545 (t80) REVERT: F 211 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8829 (ttp) outliers start: 27 outliers final: 20 residues processed: 187 average time/residue: 0.1101 time to fit residues: 30.4513 Evaluate side-chains 175 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 182 GLN Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 121 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 chunk 26 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124417 restraints weight = 15693.441| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.63 r_work: 0.3039 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 13486 Z= 0.121 Angle : 0.706 15.812 18352 Z= 0.324 Chirality : 0.044 0.159 1914 Planarity : 0.005 0.063 2207 Dihedral : 16.895 175.170 1991 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.60 % Favored : 90.26 % Rotamer: Outliers : 2.60 % Allowed : 12.17 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.63 (0.22), residues: 1510 helix: 0.40 (0.19), residues: 788 sheet: -2.65 (1.12), residues: 20 loop : -2.92 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.014 0.001 TYR E 249 PHE 0.017 0.001 PHE E 320 TRP 0.010 0.001 TRP E 183 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00278 (13464) covalent geometry : angle 0.69209 (18342) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.35003 ( 4) hydrogen bonds : bond 0.03737 ( 554) hydrogen bonds : angle 4.32513 ( 1626) metal coordination : bond 0.01071 ( 8) metal coordination : angle 7.78935 ( 6) Misc. bond : bond 0.05966 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6529 (p0) REVERT: B 12 ASP cc_start: 0.8265 (t0) cc_final: 0.7867 (t0) REVERT: B 18 ARG cc_start: 0.7110 (mtp180) cc_final: 0.6047 (mmp-170) REVERT: B 99 MET cc_start: 0.9036 (mmm) cc_final: 0.8643 (mmm) REVERT: C 63 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7856 (ttt-90) REVERT: C 113 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7185 (ptp90) REVERT: C 224 LEU cc_start: 0.8179 (pp) cc_final: 0.7952 (mt) REVERT: D 103 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6547 (p0) REVERT: E 12 ASP cc_start: 0.8265 (t0) cc_final: 0.7876 (t0) REVERT: E 18 ARG cc_start: 0.6957 (mtp180) cc_final: 0.5933 (mmp-170) REVERT: E 99 MET cc_start: 0.9033 (mmm) cc_final: 0.8638 (mmm) REVERT: F 113 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7182 (ptp90) REVERT: F 118 LYS cc_start: 0.8461 (tttm) cc_final: 0.8124 (ttpt) REVERT: F 224 LEU cc_start: 0.8200 (pp) cc_final: 0.7965 (mt) outliers start: 34 outliers final: 21 residues processed: 208 average time/residue: 0.1002 time to fit residues: 31.6289 Evaluate side-chains 174 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 0.0050 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN F 176 ASN F 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.157410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.124785 restraints weight = 15716.239| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.42 r_work: 0.3012 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13486 Z= 0.129 Angle : 0.700 15.761 18352 Z= 0.319 Chirality : 0.045 0.172 1914 Planarity : 0.005 0.052 2207 Dihedral : 16.606 172.643 1987 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.00 % Favored : 89.87 % Rotamer: Outliers : 3.91 % Allowed : 13.09 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.28 (0.22), residues: 1510 helix: 0.65 (0.19), residues: 798 sheet: -2.44 (1.13), residues: 20 loop : -2.74 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.014 0.001 TYR E 249 PHE 0.016 0.001 PHE F 25 TRP 0.009 0.001 TRP E 183 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00314 (13464) covalent geometry : angle 0.68511 (18342) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.35395 ( 4) hydrogen bonds : bond 0.03637 ( 554) hydrogen bonds : angle 4.16338 ( 1626) metal coordination : bond 0.01096 ( 8) metal coordination : angle 8.00931 ( 6) Misc. bond : bond 0.03825 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7623 (ttt90) cc_final: 0.7321 (ttt90) REVERT: A 103 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6560 (p0) REVERT: B 12 ASP cc_start: 0.8250 (t0) cc_final: 0.7855 (t0) REVERT: B 18 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6027 (mmp-170) REVERT: C 224 LEU cc_start: 0.8220 (pp) cc_final: 0.7934 (mt) REVERT: D 71 ARG cc_start: 0.7501 (ttt90) cc_final: 0.7227 (ttt90) REVERT: D 103 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6648 (p0) REVERT: E 12 ASP cc_start: 0.8224 (t0) cc_final: 0.7849 (t0) REVERT: E 18 ARG cc_start: 0.6999 (mtp180) cc_final: 0.5970 (mmp-170) REVERT: F 63 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7906 (ttt-90) REVERT: F 113 ARG cc_start: 0.7946 (ptp90) cc_final: 0.7277 (ptp90) REVERT: F 224 LEU cc_start: 0.8221 (pp) cc_final: 0.7930 (mt) outliers start: 51 outliers final: 28 residues processed: 209 average time/residue: 0.1026 time to fit residues: 31.7871 Evaluate side-chains 186 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 182 GLN Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.152289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118425 restraints weight = 15671.658| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.28 r_work: 0.3010 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 13486 Z= 0.149 Angle : 0.730 16.981 18352 Z= 0.325 Chirality : 0.045 0.168 1914 Planarity : 0.005 0.046 2207 Dihedral : 16.486 171.886 1987 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.60 % Favored : 89.27 % Rotamer: Outliers : 3.60 % Allowed : 14.40 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % 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: -1.10 (0.23), residues: 1510 helix: 0.77 (0.19), residues: 798 sheet: -2.22 (1.14), residues: 20 loop : -2.62 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 22 TYR 0.013 0.001 TYR E 249 PHE 0.018 0.001 PHE C 25 TRP 0.008 0.001 TRP B 151 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00368 (13464) covalent geometry : angle 0.71450 (18342) SS BOND : bond 0.00012 ( 2) SS BOND : angle 0.36982 ( 4) hydrogen bonds : bond 0.03702 ( 554) hydrogen bonds : angle 4.12692 ( 1626) metal coordination : bond 0.01276 ( 8) metal coordination : angle 8.36027 ( 6) Misc. bond : bond 0.06935 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7439 (ttt90) REVERT: A 103 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6621 (p0) REVERT: B 12 ASP cc_start: 0.8399 (t0) cc_final: 0.8026 (t0) REVERT: B 18 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6204 (mmp-170) REVERT: C 118 LYS cc_start: 0.8524 (tttm) cc_final: 0.8268 (ttpt) REVERT: D 71 ARG cc_start: 0.7582 (ttt90) cc_final: 0.7345 (ttt90) REVERT: D 103 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6680 (p0) REVERT: D 114 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6547 (mp) REVERT: E 12 ASP cc_start: 0.8377 (t0) cc_final: 0.7978 (t0) REVERT: E 18 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6152 (mmp-170) REVERT: F 63 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.8099 (ttt-90) REVERT: F 113 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7416 (ptp90) outliers start: 47 outliers final: 34 residues processed: 194 average time/residue: 0.1072 time to fit residues: 30.3424 Evaluate side-chains 194 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 30 optimal weight: 0.0770 chunk 84 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 ASN ** D 113 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 = 0.3727 r_free = 0.3727 target = 0.159053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125536 restraints weight = 15414.802| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.18 r_work: 0.3124 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13486 Z= 0.117 Angle : 0.677 15.606 18352 Z= 0.309 Chirality : 0.044 0.165 1914 Planarity : 0.005 0.043 2207 Dihedral : 16.088 174.052 1987 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.07 % Rotamer: Outliers : 3.22 % Allowed : 15.24 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1510 helix: 1.02 (0.19), residues: 802 sheet: -1.87 (1.21), residues: 20 loop : -2.53 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.016 0.001 TYR B 249 PHE 0.014 0.001 PHE F 25 TRP 0.007 0.001 TRP E 183 HIS 0.002 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00279 (13464) covalent geometry : angle 0.66047 (18342) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.40310 ( 4) hydrogen bonds : bond 0.03349 ( 554) hydrogen bonds : angle 3.97298 ( 1626) metal coordination : bond 0.00806 ( 8) metal coordination : angle 8.23334 ( 6) Misc. bond : bond 0.04294 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7645 (ttt90) cc_final: 0.7412 (ttt90) REVERT: A 103 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6664 (p0) REVERT: B 12 ASP cc_start: 0.8316 (t0) cc_final: 0.7934 (t0) REVERT: B 18 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6179 (mmp-170) REVERT: B 203 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8845 (t) REVERT: C 60 GLU cc_start: 0.8706 (mt-10) cc_final: 0.7899 (mm-30) REVERT: C 113 ARG cc_start: 0.7941 (ptp90) cc_final: 0.7679 (ptt180) REVERT: D 71 ARG cc_start: 0.7560 (ttt90) cc_final: 0.7349 (ttt90) REVERT: D 103 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.6564 (p0) REVERT: D 114 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6431 (mp) REVERT: E 12 ASP cc_start: 0.8265 (t0) cc_final: 0.7880 (t0) REVERT: E 18 ARG cc_start: 0.7057 (mtp180) cc_final: 0.6127 (mmp-170) REVERT: E 203 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8841 (t) REVERT: F 60 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7887 (mm-30) outliers start: 42 outliers final: 24 residues processed: 208 average time/residue: 0.1050 time to fit residues: 31.8844 Evaluate side-chains 193 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 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 = 0.3677 r_free = 0.3677 target = 0.155166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122615 restraints weight = 15585.744| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.36 r_work: 0.3047 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13486 Z= 0.118 Angle : 0.679 15.147 18352 Z= 0.311 Chirality : 0.044 0.158 1914 Planarity : 0.005 0.042 2207 Dihedral : 15.868 175.543 1987 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.06 % Allowed : 16.16 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.23), residues: 1510 helix: 1.18 (0.19), residues: 800 sheet: -1.63 (1.23), residues: 20 loop : -2.42 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 63 TYR 0.015 0.001 TYR B 249 PHE 0.013 0.001 PHE F 25 TRP 0.007 0.001 TRP B 85 HIS 0.002 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00279 (13464) covalent geometry : angle 0.66238 (18342) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.37979 ( 4) hydrogen bonds : bond 0.03301 ( 554) hydrogen bonds : angle 3.90442 ( 1626) metal coordination : bond 0.00814 ( 8) metal coordination : angle 8.19320 ( 6) Misc. bond : bond 0.04280 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7683 (ttt90) cc_final: 0.7437 (ttt90) REVERT: A 103 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6632 (p0) REVERT: B 12 ASP cc_start: 0.8417 (t0) cc_final: 0.8028 (t0) REVERT: B 18 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6206 (mmp-170) REVERT: B 343 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7930 (mtm180) REVERT: C 60 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8033 (mm-30) REVERT: C 113 ARG cc_start: 0.7904 (ptp90) cc_final: 0.7557 (ptt180) REVERT: D 71 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7430 (ttt90) REVERT: D 103 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6593 (p0) REVERT: D 114 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6343 (mp) REVERT: E 12 ASP cc_start: 0.8445 (t0) cc_final: 0.8050 (t0) REVERT: E 18 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6104 (mmp-170) REVERT: E 343 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7891 (mtm180) REVERT: F 60 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8046 (mm-30) outliers start: 40 outliers final: 33 residues processed: 201 average time/residue: 0.1101 time to fit residues: 32.3336 Evaluate side-chains 198 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.159256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 125)---------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133780 restraints weight = 15307.174| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 0.87 r_work: 0.3154 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 13486 Z= 0.128 Angle : 0.686 15.932 18352 Z= 0.314 Chirality : 0.045 0.168 1914 Planarity : 0.005 0.043 2207 Dihedral : 15.779 176.267 1987 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.27 % Favored : 90.60 % Rotamer: Outliers : 3.37 % Allowed : 16.08 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.23), residues: 1510 helix: 1.24 (0.19), residues: 800 sheet: -1.51 (1.25), residues: 20 loop : -2.39 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.014 0.001 TYR B 249 PHE 0.023 0.001 PHE F 124 TRP 0.008 0.001 TRP E 151 HIS 0.004 0.001 HIS E 202 Details of bonding type rmsd covalent geometry : bond 0.00316 (13464) covalent geometry : angle 0.66896 (18342) SS BOND : bond 0.00041 ( 2) SS BOND : angle 0.32505 ( 4) hydrogen bonds : bond 0.03419 ( 554) hydrogen bonds : angle 3.90962 ( 1626) metal coordination : bond 0.01023 ( 8) metal coordination : angle 8.33046 ( 6) Misc. bond : bond 0.04697 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7679 (ttt90) cc_final: 0.7478 (ttt90) REVERT: A 103 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6657 (p0) REVERT: B 12 ASP cc_start: 0.8443 (t0) cc_final: 0.8056 (t0) REVERT: B 18 ARG cc_start: 0.7210 (mtp180) cc_final: 0.6317 (mmp-170) REVERT: B 343 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7948 (mtm180) REVERT: C 60 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8172 (mm-30) REVERT: D 71 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7478 (ttt90) REVERT: D 103 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6551 (p0) REVERT: D 114 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6584 (mp) REVERT: E 12 ASP cc_start: 0.8447 (t0) cc_final: 0.8074 (t0) REVERT: E 18 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6229 (mmp-170) REVERT: E 343 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7927 (mtm180) REVERT: F 60 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8161 (mm-30) outliers start: 44 outliers final: 36 residues processed: 199 average time/residue: 0.1131 time to fit residues: 32.7479 Evaluate side-chains 203 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN B 373 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN E 373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117815 restraints weight = 15706.946| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.17 r_work: 0.2988 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 13486 Z= 0.175 Angle : 0.756 18.635 18352 Z= 0.341 Chirality : 0.047 0.188 1914 Planarity : 0.005 0.042 2207 Dihedral : 15.860 175.651 1987 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.07 % Favored : 89.80 % Rotamer: Outliers : 3.37 % Allowed : 15.93 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.23), residues: 1510 helix: 1.02 (0.19), residues: 802 sheet: -1.67 (1.18), residues: 20 loop : -2.46 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.011 0.001 TYR A 142 PHE 0.023 0.002 PHE F 25 TRP 0.013 0.001 TRP E 151 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00439 (13464) covalent geometry : angle 0.73739 (18342) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.32649 ( 4) hydrogen bonds : bond 0.03916 ( 554) hydrogen bonds : angle 4.05986 ( 1626) metal coordination : bond 0.01735 ( 8) metal coordination : angle 9.34601 ( 6) Misc. bond : bond 0.06502 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7616 (ttt90) cc_final: 0.7406 (ttt90) REVERT: A 103 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6564 (p0) REVERT: B 12 ASP cc_start: 0.8410 (t0) cc_final: 0.7988 (t0) REVERT: B 18 ARG cc_start: 0.7209 (mtp180) cc_final: 0.6275 (mmp-170) REVERT: C 60 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8141 (mm-30) REVERT: D 103 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6583 (p0) REVERT: E 12 ASP cc_start: 0.8402 (t0) cc_final: 0.7991 (t0) REVERT: E 18 ARG cc_start: 0.7147 (mtp180) cc_final: 0.6167 (mmp-170) REVERT: F 60 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8124 (mm-30) REVERT: F 118 LYS cc_start: 0.8629 (tttm) cc_final: 0.8280 (ttpt) outliers start: 44 outliers final: 36 residues processed: 188 average time/residue: 0.1084 time to fit residues: 29.8355 Evaluate side-chains 190 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 103 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122118 restraints weight = 15672.644| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.18 r_work: 0.3035 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 13486 Z= 0.127 Angle : 0.702 15.827 18352 Z= 0.322 Chirality : 0.045 0.173 1914 Planarity : 0.005 0.041 2207 Dihedral : 15.603 176.965 1987 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.60 % Favored : 90.26 % Rotamer: Outliers : 3.22 % Allowed : 16.46 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.23), residues: 1510 helix: 1.24 (0.19), residues: 802 sheet: -1.53 (1.21), residues: 20 loop : -2.45 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.012 0.001 TYR A 142 PHE 0.021 0.001 PHE F 124 TRP 0.006 0.001 TRP E 151 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00308 (13464) covalent geometry : angle 0.68651 (18342) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.25861 ( 4) hydrogen bonds : bond 0.03450 ( 554) hydrogen bonds : angle 3.94936 ( 1626) metal coordination : bond 0.01084 ( 8) metal coordination : angle 8.18076 ( 6) Misc. bond : bond 0.04724 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7443 (ttt90) REVERT: A 103 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6532 (p0) REVERT: B 12 ASP cc_start: 0.8451 (t0) cc_final: 0.8046 (t0) REVERT: B 18 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6199 (mmp-170) REVERT: C 60 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8138 (mm-30) REVERT: D 103 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6559 (p0) REVERT: E 12 ASP cc_start: 0.8454 (t0) cc_final: 0.8082 (t0) REVERT: E 18 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6152 (mmp-170) REVERT: F 60 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8148 (mm-30) outliers start: 42 outliers final: 34 residues processed: 185 average time/residue: 0.1057 time to fit residues: 28.7508 Evaluate side-chains 188 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 36 optimal weight: 0.0770 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 ASN ** D 113 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 = 0.3708 r_free = 0.3708 target = 0.157356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124489 restraints weight = 15440.328| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.22 r_work: 0.3110 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13486 Z= 0.121 Angle : 0.694 15.428 18352 Z= 0.318 Chirality : 0.044 0.154 1914 Planarity : 0.005 0.041 2207 Dihedral : 15.434 176.777 1987 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 3.14 % Allowed : 17.08 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.23), residues: 1510 helix: 1.35 (0.19), residues: 800 sheet: -1.47 (1.21), residues: 20 loop : -2.41 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.017 0.001 TYR E 249 PHE 0.022 0.001 PHE F 124 TRP 0.006 0.001 TRP B 85 HIS 0.002 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00295 (13464) covalent geometry : angle 0.68005 (18342) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.27277 ( 4) hydrogen bonds : bond 0.03333 ( 554) hydrogen bonds : angle 3.89968 ( 1626) metal coordination : bond 0.01104 ( 8) metal coordination : angle 7.79218 ( 6) Misc. bond : bond 0.04506 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3201.96 seconds wall clock time: 55 minutes 24.29 seconds (3324.29 seconds total)