Starting phenix.real_space_refine on Sat Sep 12 04:26:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kls_0716/09_2026/6kls_0716.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kls_0716/09_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_0716/09_2026/6kls_0716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kls_0716/09_2026/6kls_0716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kls_0716/09_2026/6kls_0716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kls_0716/09_2026/6kls_0716.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kls_0716/09_2026/6kls_0716.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kls_0716/09_2026/6kls_0716.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.47, per 1000 atoms: 0.19 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: 0.86 Conformation dependent library (CDL) restraints added in 448.2 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: 0.33 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: 1.81 Time building geometry restraints manager: 1.14 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: 7393 34.29 - 68.58: 219 68.58 - 102.87: 28 102.87 - 137.15: 9 137.15 - 171.44: 6 Dihedral angle restraints: 7655 sinusoidal: 3217 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 7652 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.120 Find NCS groups from input model: 0.240 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 18.324 171.443 4813 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/Z covalent geometry : bond 0.01411 / 0.70 (13464) covalent geometry : angle 1.21864 / 0.57 (18342) SS BOND : bond 0.00027 / 0.01 ( 2) SS BOND : angle 0.37797 / 0.25 ( 4) hydrogen bonds : bond 0.15972 / 10.53 ( 554) hydrogen bonds : angle 6.54676 / 4.58 ( 1626) metal coordination : bond 0.08243 / 4.32 ( 8) metal coordination : angle 14.60852 / 9.61 ( 6) Misc. bond : bond 0.37145 / 17.53 ( 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 : 0.369 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: 0.1178 time to fit residues: 36.3539 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 : 0.373 ------------------------------------------------------------------------------- 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... 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 = 0.3650 r_free = 0.3650 target = 0.152897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118801 restraints weight = 15833.801| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.60 r_work: 0.3044 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 13486 Z= 0.148 Angle : 0.768 16.124 18352 Z= 0.348 Chirality : 0.045 0.159 1914 Planarity : 0.005 0.068 2207 Dihedral : 16.614 175.227 1937 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.00 % Favored : 89.87 % 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: -2.36 (0.21), residues: 1510 helix: -0.27 (0.19), residues: 802 sheet: -3.01 (1.11), residues: 20 loop : -3.22 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 113 TYR 0.011 0.001 TYR E 249 PHE 0.019 0.002 PHE E 320 TRP 0.011 0.001 TRP E 183 HIS 0.008 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13464) covalent geometry : angle 0.75151 / 0.35 (18342) SS BOND : bond 0.00045 / 0.02 ( 2) SS BOND : angle 0.28128 / 0.21 ( 4) hydrogen bonds : bond 0.04358 / 2.90 ( 554) hydrogen bonds : angle 4.67114 / 3.24 ( 1626) metal coordination : bond 0.02052 / 1.07 ( 8) metal coordination : angle 8.69782 / 5.94 ( 6) Misc. bond : bond 0.08131 / 4.19 ( 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 203 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8408 (t0) cc_final: 0.7971 (t0) REVERT: B 18 ARG cc_start: 0.7012 (mtp180) cc_final: 0.6038 (mmp-170) REVERT: B 99 MET cc_start: 0.9115 (mmm) cc_final: 0.8770 (mmm) REVERT: B 259 MET cc_start: 0.9120 (mmt) cc_final: 0.8913 (mmm) REVERT: C 211 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8812 (ttp) REVERT: E 12 ASP cc_start: 0.8434 (t0) cc_final: 0.8002 (t0) REVERT: E 18 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6001 (mmp-170) REVERT: E 99 MET cc_start: 0.9108 (mmm) cc_final: 0.8759 (mmm) REVERT: F 211 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8830 (ttp) outliers start: 27 outliers final: 19 residues processed: 194 average time/residue: 0.1010 time to fit residues: 29.5259 Evaluate side-chains 171 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 121 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 GLN ** 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 = 0.3738 r_free = 0.3738 target = 0.160138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123877 restraints weight = 15686.449| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.58 r_work: 0.2998 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13486 Z= 0.128 Angle : 0.717 16.423 18352 Z= 0.327 Chirality : 0.045 0.169 1914 Planarity : 0.005 0.064 2207 Dihedral : 16.229 177.713 1937 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.87 % Favored : 90.00 % Rotamer: Outliers : 3.29 % Allowed : 11.94 % Favored : 84.76 % 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: -1.71 (0.22), residues: 1510 helix: 0.29 (0.19), residues: 794 sheet: -2.68 (1.11), residues: 20 loop : -2.92 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.013 0.001 TYR E 249 PHE 0.017 0.001 PHE F 25 TRP 0.009 0.001 TRP E 183 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (13464) covalent geometry : angle 0.70168 / 0.33 (18342) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 0.34691 / 0.24 ( 4) hydrogen bonds : bond 0.03872 / 2.59 ( 554) hydrogen bonds : angle 4.36053 / 3.03 ( 1626) metal coordination : bond 0.01379 / 0.69 ( 8) metal coordination : angle 8.10273 / 5.63 ( 6) Misc. bond : bond 0.04526 / 2.21 ( 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: 43 poor density : 173 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6537 (p0) REVERT: B 12 ASP cc_start: 0.8293 (t0) cc_final: 0.7890 (t0) REVERT: B 18 ARG cc_start: 0.7067 (mtp180) cc_final: 0.6041 (mmp-170) REVERT: B 203 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 224 LEU cc_start: 0.8236 (pp) cc_final: 0.7940 (mt) REVERT: D 103 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6560 (p0) REVERT: E 12 ASP cc_start: 0.8277 (t0) cc_final: 0.7881 (t0) REVERT: E 18 ARG cc_start: 0.6974 (mtp180) cc_final: 0.5955 (mmp-170) REVERT: E 203 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8857 (t) REVERT: F 118 LYS cc_start: 0.8476 (tttm) cc_final: 0.8137 (ttpt) REVERT: F 224 LEU cc_start: 0.8231 (pp) cc_final: 0.7933 (mt) outliers start: 43 outliers final: 24 residues processed: 206 average time/residue: 0.1046 time to fit residues: 32.2314 Evaluate side-chains 176 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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 160 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 176 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 203 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 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: 0.8980 chunk 37 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 176 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.154961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 161)---------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116973 restraints weight = 15810.274| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.62 r_work: 0.2990 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13486 Z= 0.138 Angle : 0.713 16.322 18352 Z= 0.326 Chirality : 0.045 0.176 1914 Planarity : 0.005 0.054 2207 Dihedral : 15.888 173.664 1937 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.40 % Favored : 89.47 % Rotamer: Outliers : 3.37 % Allowed : 14.32 % Favored : 82.31 % 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: -1.34 (0.22), residues: 1510 helix: 0.56 (0.19), residues: 796 sheet: -2.44 (1.10), residues: 20 loop : -2.71 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 113 TYR 0.014 0.001 TYR E 249 PHE 0.018 0.001 PHE F 25 TRP 0.008 0.001 TRP B 183 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13464) covalent geometry : angle 0.69732 / 0.33 (18342) SS BOND : bond 0.00025 / 0.01 ( 2) SS BOND : angle 0.33759 / 0.20 ( 4) hydrogen bonds : bond 0.03751 / 2.49 ( 554) hydrogen bonds : angle 4.20845 / 2.92 ( 1626) metal coordination : bond 0.01090 / 0.54 ( 8) metal coordination : angle 8.27828 / 5.81 ( 6) Misc. bond : bond 0.03852 / 1.99 ( 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 207 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7611 (ttt90) cc_final: 0.7304 (ttt90) REVERT: A 103 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6612 (p0) REVERT: B 12 ASP cc_start: 0.8251 (t0) cc_final: 0.7842 (t0) REVERT: B 18 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6026 (mmp-170) REVERT: C 113 ARG cc_start: 0.7949 (ptt180) cc_final: 0.7666 (ptp-170) REVERT: D 71 ARG cc_start: 0.7485 (ttt90) cc_final: 0.7183 (ttt90) REVERT: D 103 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6687 (p0) REVERT: E 12 ASP cc_start: 0.8235 (t0) cc_final: 0.7841 (t0) REVERT: E 18 ARG cc_start: 0.7014 (mtp180) cc_final: 0.5956 (mmp-170) REVERT: F 113 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7680 (ptp-170) outliers start: 44 outliers final: 30 residues processed: 193 average time/residue: 0.1086 time to fit residues: 31.4149 Evaluate side-chains 183 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 106 MET 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 84 MET Chi-restraints excluded: chain C residue 96 GLU 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 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 106 MET 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 F residue 84 MET Chi-restraints excluded: chain F residue 113 ARG 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: 0.8980 chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.155572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.125042 restraints weight = 15869.440| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.17 r_work: 0.3028 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1879 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= 0.133 Angle : 0.701 16.893 18352 Z= 0.321 Chirality : 0.045 0.171 1914 Planarity : 0.005 0.047 2207 Dihedral : 15.738 173.079 1933 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.26 % Favored : 89.60 % Rotamer: Outliers : 3.37 % Allowed : 14.85 % Favored : 81.78 % 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: -1.17 (0.22), residues: 1510 helix: 0.72 (0.19), residues: 798 sheet: -2.20 (1.11), residues: 20 loop : -2.68 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 113 TYR 0.014 0.001 TYR A 142 PHE 0.017 0.001 PHE F 25 TRP 0.007 0.001 TRP B 151 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (13464) covalent geometry : angle 0.68446 / 0.32 (18342) SS BOND : bond 0.00026 / 0.01 ( 2) SS BOND : angle 0.37147 / 0.24 ( 4) hydrogen bonds : bond 0.03616 / 2.40 ( 554) hydrogen bonds : angle 4.13765 / 2.88 ( 1626) metal coordination : bond 0.01082 / 0.55 ( 8) metal coordination : angle 8.42315 / 5.80 ( 6) Misc. bond : bond 0.03655 / 1.89 ( 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 204 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7378 (ttt90) REVERT: A 103 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6619 (p0) REVERT: B 12 ASP cc_start: 0.8255 (t0) cc_final: 0.7877 (t0) REVERT: B 18 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6062 (mmp-170) REVERT: C 113 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7758 (ptp-170) REVERT: C 118 LYS cc_start: 0.8552 (tttm) cc_final: 0.8193 (ttpt) REVERT: C 224 LEU cc_start: 0.8274 (pp) cc_final: 0.7954 (mt) REVERT: D 71 ARG cc_start: 0.7527 (ttt90) cc_final: 0.7287 (ttt90) REVERT: D 103 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6666 (p0) REVERT: D 114 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6304 (mp) REVERT: E 12 ASP cc_start: 0.8206 (t0) cc_final: 0.7808 (t0) REVERT: E 18 ARG cc_start: 0.7041 (mtp180) cc_final: 0.6015 (mmp-170) REVERT: F 224 LEU cc_start: 0.8289 (pp) cc_final: 0.7970 (mt) outliers start: 44 outliers final: 33 residues processed: 189 average time/residue: 0.1137 time to fit residues: 31.8401 Evaluate side-chains 192 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 106 MET 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 96 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 113 ARG 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 106 MET 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 346 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.156202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124225 restraints weight = 15702.316| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.04 r_work: 0.3044 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 13486 Z= 0.138 Angle : 0.698 16.994 18352 Z= 0.321 Chirality : 0.045 0.175 1914 Planarity : 0.005 0.045 2207 Dihedral : 15.590 173.889 1933 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.00 % Favored : 89.87 % Rotamer: Outliers : 3.91 % Allowed : 15.54 % 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: -1.03 (0.23), residues: 1510 helix: 0.83 (0.19), residues: 802 sheet: -1.91 (1.16), residues: 20 loop : -2.63 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 113 TYR 0.014 0.001 TYR E 249 PHE 0.017 0.001 PHE F 25 TRP 0.008 0.001 TRP B 151 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (13464) covalent geometry : angle 0.68135 / 0.32 (18342) SS BOND : bond 0.00025 / 0.01 ( 2) SS BOND : angle 0.40983 / 0.26 ( 4) hydrogen bonds : bond 0.03621 / 2.41 ( 554) hydrogen bonds : angle 4.08054 / 2.84 ( 1626) metal coordination : bond 0.01136 / 0.58 ( 8) metal coordination : angle 8.51221 / 5.92 ( 6) Misc. bond : bond 0.03961 / 2.02 ( 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: 51 poor density : 164 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7395 (ttt90) REVERT: A 103 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6616 (p0) REVERT: B 12 ASP cc_start: 0.8250 (t0) cc_final: 0.7852 (t0) REVERT: B 18 ARG cc_start: 0.7131 (mtp180) cc_final: 0.6102 (mmp-170) REVERT: C 60 GLU cc_start: 0.8666 (mt-10) cc_final: 0.7993 (mm-30) REVERT: C 113 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7736 (ptp-170) REVERT: C 224 LEU cc_start: 0.8300 (pp) cc_final: 0.8009 (mt) REVERT: D 71 ARG cc_start: 0.7521 (ttt90) cc_final: 0.7294 (ttt90) REVERT: D 103 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6620 (p0) REVERT: D 114 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6355 (mp) REVERT: E 12 ASP cc_start: 0.8212 (t0) cc_final: 0.7824 (t0) REVERT: E 18 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6068 (mmp-170) REVERT: F 60 GLU cc_start: 0.8673 (mt-10) cc_final: 0.7980 (mm-30) REVERT: F 224 LEU cc_start: 0.8295 (pp) cc_final: 0.8003 (mt) outliers start: 51 outliers final: 36 residues processed: 201 average time/residue: 0.1126 time to fit residues: 33.7396 Evaluate side-chains 195 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 106 MET 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 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 113 ARG Chi-restraints excluded: chain C residue 122 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 65 SER Chi-restraints excluded: chain E residue 106 MET 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 346 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 122 GLU 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: 0.0670 chunk 113 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 71 optimal weight: 0.0370 chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 8 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3725 r_free = 0.3725 target = 0.159115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.128363 restraints weight = 15508.081| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.11 r_work: 0.3170 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13486 Z= 0.115 Angle : 0.673 14.826 18352 Z= 0.312 Chirality : 0.044 0.157 1914 Planarity : 0.005 0.042 2207 Dihedral : 15.236 176.436 1933 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 2.53 % Allowed : 17.53 % Favored : 79.94 % 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: -0.71 (0.23), residues: 1510 helix: 1.12 (0.19), residues: 802 sheet: -1.56 (1.23), residues: 20 loop : -2.51 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.017 0.001 TYR B 249 PHE 0.016 0.001 PHE F 179 TRP 0.007 0.001 TRP B 123 HIS 0.002 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (13464) covalent geometry : angle 0.65758 / 0.31 (18342) SS BOND : bond 0.00010 / 0.01 ( 2) SS BOND : angle 0.42982 / 0.26 ( 4) hydrogen bonds : bond 0.03267 / 2.20 ( 554) hydrogen bonds : angle 3.91757 / 2.72 ( 1626) metal coordination : bond 0.00708 / 0.35 ( 8) metal coordination : angle 8.02802 / 5.39 ( 6) Misc. bond : bond 0.03639 / 1.72 ( 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 217 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7711 (ttt90) cc_final: 0.7495 (ttt90) REVERT: A 103 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6718 (p0) REVERT: B 12 ASP cc_start: 0.8456 (t0) cc_final: 0.8067 (t0) REVERT: B 18 ARG cc_start: 0.7309 (mtp180) cc_final: 0.6334 (mmp-170) REVERT: B 343 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7949 (mtm180) REVERT: C 60 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8010 (mm-30) REVERT: D 71 ARG cc_start: 0.7690 (ttt90) cc_final: 0.7466 (ttt90) REVERT: D 103 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6682 (p0) REVERT: D 114 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6539 (mp) REVERT: E 12 ASP cc_start: 0.8394 (t0) cc_final: 0.8019 (t0) REVERT: E 18 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6164 (mmp-170) REVERT: E 343 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7916 (mtm180) REVERT: F 60 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8012 (mm-30) outliers start: 33 outliers final: 21 residues processed: 204 average time/residue: 0.1164 time to fit residues: 34.7519 Evaluate side-chains 191 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 106 MET 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 395 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN 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 106 MET 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 395 SER Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR 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: 0.2980 chunk 8 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3660 r_free = 0.3660 target = 0.153839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120177 restraints weight = 15559.866| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.24 r_work: 0.3048 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13486 Z= 0.129 Angle : 0.681 15.593 18352 Z= 0.314 Chirality : 0.045 0.177 1914 Planarity : 0.005 0.042 2207 Dihedral : 15.170 176.618 1933 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.93 % Favored : 90.00 % Rotamer: Outliers : 2.99 % Allowed : 17.38 % Favored : 79.63 % 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: -0.65 (0.23), residues: 1510 helix: 1.17 (0.19), residues: 802 sheet: -1.37 (1.26), residues: 20 loop : -2.51 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 22 TYR 0.012 0.001 TYR A 142 PHE 0.021 0.001 PHE F 124 TRP 0.008 0.001 TRP B 151 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (13464) covalent geometry : angle 0.66597 / 0.31 (18342) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 0.61504 / 0.40 ( 4) hydrogen bonds : bond 0.03400 / 2.27 ( 554) hydrogen bonds : angle 3.92171 / 2.73 ( 1626) metal coordination : bond 0.01258 / 0.63 ( 8) metal coordination : angle 7.91336 / 5.53 ( 6) Misc. bond : bond 0.04131 / 2.12 ( 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: 39 poor density : 170 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7454 (ttt90) REVERT: A 103 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6687 (p0) REVERT: B 12 ASP cc_start: 0.8462 (t0) cc_final: 0.8046 (t0) REVERT: B 18 ARG cc_start: 0.7193 (mtp180) cc_final: 0.6180 (mmp-170) REVERT: B 209 ILE cc_start: 0.8554 (pt) cc_final: 0.8314 (mt) REVERT: B 343 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7920 (mtm180) REVERT: C 60 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8105 (mm-30) REVERT: D 71 ARG cc_start: 0.7685 (ttt90) cc_final: 0.7460 (ttt90) REVERT: D 103 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6543 (p0) REVERT: D 114 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6356 (mp) REVERT: E 12 ASP cc_start: 0.8433 (t0) cc_final: 0.8039 (t0) REVERT: E 18 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6128 (mmp-170) REVERT: E 343 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7867 (mtm180) REVERT: F 60 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8077 (mm-30) outliers start: 39 outliers final: 29 residues processed: 196 average time/residue: 0.1170 time to fit residues: 33.5985 Evaluate side-chains 200 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 113 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 106 MET 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 310 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN 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 106 MET 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 395 SER Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 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: 0.7980 chunk 134 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN E 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.153967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121640 restraints weight = 15613.187| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.29 r_work: 0.3037 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13486 Z= 0.127 Angle : 0.682 15.503 18352 Z= 0.315 Chirality : 0.045 0.177 1914 Planarity : 0.005 0.042 2207 Dihedral : 15.025 176.813 1933 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.74 % Favored : 90.13 % Rotamer: Outliers : 2.60 % Allowed : 17.61 % 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: -0.60 (0.23), residues: 1510 helix: 1.25 (0.19), residues: 802 sheet: -1.38 (1.26), residues: 20 loop : -2.52 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 117 TYR 0.012 0.001 TYR A 142 PHE 0.021 0.001 PHE F 124 TRP 0.008 0.001 TRP B 151 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (13464) covalent geometry : angle 0.66822 / 0.31 (18342) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 0.46195 / 0.28 ( 4) hydrogen bonds : bond 0.03353 / 2.24 ( 554) hydrogen bonds : angle 3.91011 / 2.72 ( 1626) metal coordination : bond 0.01029 / 0.51 ( 8) metal coordination : angle 7.70619 / 5.35 ( 6) Misc. bond : bond 0.04058 / 2.12 ( 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 207 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7699 (ttt90) cc_final: 0.7479 (ttt90) REVERT: A 103 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6708 (p0) REVERT: B 12 ASP cc_start: 0.8499 (t0) cc_final: 0.8084 (t0) REVERT: B 18 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6151 (mmp-170) REVERT: B 209 ILE cc_start: 0.8583 (pt) cc_final: 0.8333 (mt) REVERT: B 343 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7921 (mtm180) REVERT: C 60 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8139 (mm-30) REVERT: D 71 ARG cc_start: 0.7732 (ttt90) cc_final: 0.7506 (ttt90) REVERT: D 103 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6558 (p0) REVERT: D 114 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6481 (mp) REVERT: E 12 ASP cc_start: 0.8444 (t0) cc_final: 0.8042 (t0) REVERT: E 18 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6096 (mmp-170) REVERT: E 343 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7885 (mtm180) REVERT: F 60 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8120 (mm-30) outliers start: 34 outliers final: 29 residues processed: 197 average time/residue: 0.1184 time to fit residues: 34.0827 Evaluate side-chains 201 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 113 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 106 MET 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 395 SER Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 182 GLN 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 106 MET 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 176 ILE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 103 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN E 321 ASN F 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.159259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3360 r_free = 0.3360 target = 0.127334 restraints weight = 15512.851| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.22 r_work: 0.3082 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 13486 Z= 0.135 Angle : 0.695 15.602 18352 Z= 0.321 Chirality : 0.045 0.189 1914 Planarity : 0.005 0.041 2207 Dihedral : 14.943 176.466 1933 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.60 % Favored : 90.26 % Rotamer: Outliers : 2.91 % Allowed : 17.46 % Favored : 79.63 % 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: 1.27 (0.19), residues: 800 sheet: -1.37 (1.25), residues: 20 loop : -2.49 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 63 TYR 0.012 0.001 TYR A 142 PHE 0.021 0.001 PHE F 124 TRP 0.008 0.001 TRP B 151 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.13 (13464) covalent geometry : angle 0.68148 / 0.32 (18342) SS BOND : bond 0.00037 / 0.02 ( 2) SS BOND : angle 0.43517 / 0.27 ( 4) hydrogen bonds : bond 0.03443 / 2.29 ( 554) hydrogen bonds : angle 3.93296 / 2.74 ( 1626) metal coordination : bond 0.01086 / 0.55 ( 8) metal coordination : angle 7.62625 / 5.25 ( 6) Misc. bond : bond 0.04368 / 2.32 ( 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 205 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7426 (ttt90) REVERT: A 103 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6598 (p0) REVERT: B 12 ASP cc_start: 0.8308 (t0) cc_final: 0.7900 (t0) REVERT: B 18 ARG cc_start: 0.7079 (mtp180) cc_final: 0.6092 (mmp-170) REVERT: B 209 ILE cc_start: 0.8561 (pt) cc_final: 0.8346 (mt) REVERT: B 343 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7867 (mtm180) REVERT: C 60 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8017 (mm-30) REVERT: D 71 ARG cc_start: 0.7652 (ttt90) cc_final: 0.7422 (ttt90) REVERT: D 103 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6562 (p0) REVERT: D 114 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6395 (mp) REVERT: E 12 ASP cc_start: 0.8263 (t0) cc_final: 0.7868 (t0) REVERT: E 18 ARG cc_start: 0.7038 (mtp180) cc_final: 0.6054 (mmp-170) REVERT: E 343 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7848 (mtm180) REVERT: F 60 GLU cc_start: 0.8628 (mt-10) cc_final: 0.7998 (mm-30) outliers start: 38 outliers final: 31 residues processed: 195 average time/residue: 0.1162 time to fit residues: 33.4921 Evaluate side-chains 199 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 113 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 106 MET 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 395 SER Chi-restraints excluded: chain C residue 32 VAL 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 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 106 MET 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 176 ILE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 170 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 321 ASN E 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.153244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121971 restraints weight = 15509.043| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 0.99 r_work: 0.3080 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 13486 Z= 0.131 Angle : 0.693 14.800 18352 Z= 0.321 Chirality : 0.045 0.177 1914 Planarity : 0.005 0.041 2207 Dihedral : 14.855 176.170 1933 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.07 % Favored : 89.80 % Rotamer: Outliers : 2.83 % Allowed : 17.92 % Favored : 79.25 % 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: -0.52 (0.23), residues: 1510 helix: 1.31 (0.19), residues: 800 sheet: -1.33 (1.26), residues: 20 loop : -2.47 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 117 TYR 0.012 0.001 TYR A 142 PHE 0.022 0.001 PHE F 124 TRP 0.008 0.001 TRP B 151 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (13464) covalent geometry : angle 0.68048 / 0.32 (18342) SS BOND : bond 0.00048 / 0.03 ( 2) SS BOND : angle 0.43295 / 0.27 ( 4) hydrogen bonds : bond 0.03392 / 2.26 ( 554) hydrogen bonds : angle 3.92128 / 2.73 ( 1626) metal coordination : bond 0.01066 / 0.54 ( 8) metal coordination : angle 7.31214 / 4.97 ( 6) Misc. bond : bond 0.04476 / 2.36 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.28 seconds wall clock time: 59 minutes 34.18 seconds (3574.18 seconds total)