Starting phenix.real_space_refine on Fri Sep 11 15:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pr5_20457/09_2026/6pr5_20457.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 124 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 6073 2.51 5 N 1773 2.21 5 O 2182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.00s 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: 10194 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3823 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 324 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 181 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 755 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1720 SG CYS A 240 28.075 20.995 56.182 1.00 66.94 S ATOM 1746 SG CYS A 243 26.675 18.929 53.984 1.00 66.43 S ATOM 5543 SG CYS E 240 66.736 74.745 53.312 1.00 75.78 S ATOM 5569 SG CYS E 243 68.439 75.903 50.736 1.00 75.72 S Time building chain proxies: 2.07, per 1000 atoms: 0.20 Number of scatterers: 10194 At special positions: 0 Unit cell: (97.65, 101.85, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 124 15.00 Mg 4 11.99 O 2182 8.00 N 1773 7.00 C 6073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 264.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 240 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 408 " pdb="ZN ZN E 603 " - pdb=" NE2 HIS E 413 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 243 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 240 " Number of angles added : 4 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 53.3% alpha, 15.0% beta 60 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.535A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.802A pdb=" N ILE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.737A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 289 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.536A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.572A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.764A pdb=" N ASN A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.583A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.749A pdb=" N THR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.796A pdb=" N SER E 251 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 271 through 289 removed outlier: 3.675A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 322 Processing helix chain 'E' and resid 337 through 347 removed outlier: 4.653A pdb=" N PHE E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 413 through 421 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.808A pdb=" N LYS E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.665A pdb=" N THR E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 164 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 158 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.340A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 116 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS A 217 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 118 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET A 219 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 120 " --> pdb=" O MET A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.128A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP E 164 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA E 158 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR E 162 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.723A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 119 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 156 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 117 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU E 116 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LYS E 217 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 118 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET E 219 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER E 120 " --> pdb=" O MET E 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'E' and resid 377 through 378 removed outlier: 4.145A pdb=" N ILE E 377 " --> pdb=" O GLN E 497 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 298 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2124 1.33 - 1.45: 2836 1.45 - 1.57: 5380 1.57 - 1.69: 242 1.69 - 1.81: 56 Bond restraints: 10638 Sorted by residual: bond pdb=" C3' DC B 17 " pdb=" O3' DC B 17 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" N1 DC D 12 " pdb=" C6 DC D 12 " ideal model delta sigma weight residual 1.367 1.346 0.021 6.00e-03 2.78e+04 1.21e+01 bond pdb=" C3' DC G 19 " pdb=" O3' DC G 19 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.21e+01 bond pdb=" C3' DC D 12 " pdb=" O3' DC D 12 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C3' DA F 7 " pdb=" O3' DA F 7 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 10633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14388 2.11 - 4.21: 465 4.21 - 6.32: 28 6.32 - 8.43: 9 8.43 - 10.53: 2 Bond angle restraints: 14892 Sorted by residual: angle pdb=" C ASP E 379 " pdb=" N VAL E 380 " pdb=" CA VAL E 380 " ideal model delta sigma weight residual 120.24 123.50 -3.26 6.30e-01 2.52e+00 2.68e+01 angle pdb=" O4' DC H 12 " pdb=" C4' DC H 12 " pdb=" C3' DC H 12 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" O4' DA G 18 " pdb=" C4' DA G 18 " pdb=" C3' DA G 18 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT H 22 " pdb=" C4 DT H 22 " pdb=" O4 DT H 22 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.08e+01 ... (remaining 14887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 5430 32.04 - 64.08: 673 64.08 - 96.12: 24 96.12 - 128.15: 1 128.15 - 160.19: 2 Dihedral angle restraints: 6130 sinusoidal: 3302 harmonic: 2828 Sorted by residual: dihedral pdb=" CA GLY E 427 " pdb=" C GLY E 427 " pdb=" N SER E 428 " pdb=" CA SER E 428 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY A 427 " pdb=" C GLY A 427 " pdb=" N SER A 428 " pdb=" CA SER A 428 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU A 138 " pdb=" C GLU A 138 " pdb=" N SER A 139 " pdb=" CA SER A 139 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1292 0.058 - 0.117: 335 0.117 - 0.175: 57 0.175 - 0.233: 3 0.233 - 0.291: 3 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA GLU E 138 " pdb=" N GLU E 138 " pdb=" C GLU E 138 " pdb=" CB GLU E 138 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3' DA F 7 " pdb=" C4' DA F 7 " pdb=" O3' DA F 7 " pdb=" C2' DA F 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB THR E 334 " pdb=" CA THR E 334 " pdb=" OG1 THR E 334 " pdb=" CG2 THR E 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1687 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT F 2 " -0.008 2.00e-02 2.50e+03 1.57e-02 6.19e+00 pdb=" N1 DT F 2 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DT F 2 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT F 2 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT F 2 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DT F 2 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT F 2 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT F 2 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT F 2 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 11 " -0.027 2.00e-02 2.50e+03 1.44e-02 5.73e+00 pdb=" N9 DA D 11 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA D 11 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA D 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA D 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 11 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA D 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA D 11 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA D 11 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 16 " -0.001 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" N1 DT B 16 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DT B 16 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT B 16 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT B 16 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT B 16 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT B 16 " -0.034 2.00e-02 2.50e+03 pdb=" C7 DT B 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT B 16 " 0.026 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 95 2.55 - 3.14: 8049 3.14 - 3.73: 17032 3.73 - 4.31: 23758 4.31 - 4.90: 37759 Nonbonded interactions: 86693 Sorted by model distance: nonbonded pdb=" O3' DC F 9 " pdb="MG MG E 601 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASP E 125 " pdb="MG MG E 601 " model vdw 2.123 2.170 nonbonded pdb=" OD2 ASP E 125 " pdb="MG MG E 602 " model vdw 2.133 2.170 nonbonded pdb=" OD2 ASP E 224 " pdb="MG MG E 601 " model vdw 2.138 2.170 nonbonded pdb=" OE1 GLU E 435 " pdb="MG MG E 602 " model vdw 2.149 2.170 ... (remaining 86688 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 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.010 0.425 10646 Z= 0.610 Angle : 0.911 30.834 14896 Z= 0.626 Chirality : 0.053 0.291 1690 Planarity : 0.004 0.039 1452 Dihedral : 22.941 160.193 4294 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.36 % Favored : 98.33 % Rotamer: Outliers : 0.71 % Allowed : 10.47 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.21), residues: 956 helix: -1.83 (0.19), residues: 506 sheet: -1.05 (0.60), residues: 64 loop : -2.71 (0.23), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 477 TYR 0.012 0.002 TYR E 394 PHE 0.015 0.002 PHE A 292 TRP 0.017 0.002 TRP A 41 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.58 (10638) covalent geometry : angle 0.84666 / 0.62 (14892) hydrogen bonds : bond 0.11626 / 7.17 ( 520) hydrogen bonds : angle 6.07128 / 4.15 ( 1411) metal coordination : bond 0.19508 / 13.07 ( 8) metal coordination : angle 20.53761 / 9.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8418 (p0) cc_final: 0.8170 (p0) REVERT: A 212 HIS cc_start: 0.7804 (m90) cc_final: 0.7395 (m170) REVERT: E 173 MET cc_start: 0.7294 (mtp) cc_final: 0.6998 (mtp) REVERT: E 184 LYS cc_start: 0.8311 (tttt) cc_final: 0.7833 (tppt) REVERT: E 295 TRP cc_start: 0.8549 (t60) cc_final: 0.8293 (t-100) REVERT: E 423 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8101 (tt) outliers start: 6 outliers final: 4 residues processed: 116 average time/residue: 0.1013 time to fit residues: 16.3952 Evaluate side-chains 80 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 355 THR Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS A 339 ASN A 448 HIS A 486 GLN E 71 GLN E 91 GLN E 130 GLN E 136 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS E 216 HIS E 322 ASN E 330 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109144 restraints weight = 16066.859| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.99 r_work: 0.3354 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10646 Z= 0.187 Angle : 0.678 10.893 14896 Z= 0.382 Chirality : 0.044 0.213 1690 Planarity : 0.004 0.043 1452 Dihedral : 26.138 164.421 2392 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 1.88 % Allowed : 13.06 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.24), residues: 956 helix: -0.41 (0.22), residues: 512 sheet: -1.04 (0.59), residues: 64 loop : -2.24 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.016 0.001 TYR E 241 PHE 0.013 0.002 PHE A 124 TRP 0.016 0.001 TRP A 41 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (10638) covalent geometry : angle 0.67369 / 0.38 (14892) hydrogen bonds : bond 0.05205 / 3.30 ( 520) hydrogen bonds : angle 4.79631 / 3.28 ( 1411) metal coordination : bond 0.01570 / 0.84 ( 8) metal coordination : angle 4.48698 / 2.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.8755 (p) cc_final: 0.8382 (m) REVERT: A 470 ASP cc_start: 0.9051 (t70) cc_final: 0.8826 (t70) REVERT: E 106 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7701 (mmt180) REVERT: E 173 MET cc_start: 0.7931 (mtp) cc_final: 0.7567 (mtp) REVERT: E 184 LYS cc_start: 0.8457 (tttt) cc_final: 0.7604 (tptp) REVERT: E 307 HIS cc_start: 0.8179 (m90) cc_final: 0.7923 (m90) REVERT: E 423 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8205 (tt) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.0865 time to fit residues: 12.9184 Evaluate side-chains 87 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111285 restraints weight = 16185.973| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.97 r_work: 0.3359 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10646 Z= 0.166 Angle : 0.634 9.791 14896 Z= 0.360 Chirality : 0.043 0.215 1690 Planarity : 0.004 0.044 1452 Dihedral : 26.072 164.549 2391 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 2.71 % Allowed : 16.12 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.26), residues: 956 helix: 0.50 (0.23), residues: 498 sheet: -1.06 (0.59), residues: 64 loop : -1.90 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 437 TYR 0.018 0.001 TYR E 241 PHE 0.013 0.002 PHE A 292 TRP 0.015 0.001 TRP A 41 HIS 0.003 0.001 HIS E 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (10638) covalent geometry : angle 0.63300 / 0.36 (14892) hydrogen bonds : bond 0.04605 / 2.92 ( 520) hydrogen bonds : angle 4.44284 / 3.05 ( 1411) metal coordination : bond 0.00729 / 0.41 ( 8) metal coordination : angle 2.53580 / 1.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.8747 (p) cc_final: 0.8426 (m) REVERT: A 199 ASP cc_start: 0.8351 (t0) cc_final: 0.7979 (m-30) REVERT: A 219 MET cc_start: 0.8883 (ptm) cc_final: 0.8656 (ptm) REVERT: A 315 ASP cc_start: 0.8282 (m-30) cc_final: 0.7952 (m-30) REVERT: A 470 ASP cc_start: 0.9017 (t70) cc_final: 0.8752 (t70) REVERT: E 106 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7808 (mmt180) REVERT: E 173 MET cc_start: 0.7826 (mtp) cc_final: 0.7479 (mtp) REVERT: E 184 LYS cc_start: 0.8494 (tttt) cc_final: 0.7655 (tptp) REVERT: E 307 HIS cc_start: 0.8253 (m90) cc_final: 0.7914 (m90) REVERT: E 336 ASN cc_start: 0.8183 (m-40) cc_final: 0.7964 (m-40) REVERT: E 423 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8048 (tt) outliers start: 23 outliers final: 15 residues processed: 102 average time/residue: 0.0728 time to fit residues: 11.2587 Evaluate side-chains 95 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.137087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111339 restraints weight = 16348.115| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.90 r_work: 0.3361 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10646 Z= 0.180 Angle : 0.635 9.755 14896 Z= 0.357 Chirality : 0.042 0.224 1690 Planarity : 0.004 0.038 1452 Dihedral : 26.101 166.006 2391 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 2.82 % Allowed : 17.88 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.27), residues: 956 helix: 0.85 (0.24), residues: 500 sheet: -1.02 (0.58), residues: 64 loop : -1.85 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 437 TYR 0.020 0.001 TYR E 241 PHE 0.012 0.001 PHE A 180 TRP 0.013 0.001 TRP A 41 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (10638) covalent geometry : angle 0.63390 / 0.36 (14892) hydrogen bonds : bond 0.04551 / 2.90 ( 520) hydrogen bonds : angle 4.32768 / 2.98 ( 1411) metal coordination : bond 0.00847 / 0.46 ( 8) metal coordination : angle 2.29459 / 1.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.336 Fit side-chains REVERT: A 145 SER cc_start: 0.8900 (p) cc_final: 0.8555 (m) REVERT: A 219 MET cc_start: 0.9069 (ptm) cc_final: 0.8837 (ptm) REVERT: A 315 ASP cc_start: 0.8462 (m-30) cc_final: 0.8134 (m-30) REVERT: A 470 ASP cc_start: 0.9079 (t70) cc_final: 0.8810 (t70) REVERT: E 57 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6471 (pt0) REVERT: E 106 ARG cc_start: 0.8064 (mmt180) cc_final: 0.7790 (mmt180) REVERT: E 173 MET cc_start: 0.8010 (mtp) cc_final: 0.7651 (mtp) REVERT: E 184 LYS cc_start: 0.8570 (tttt) cc_final: 0.7715 (tptp) REVERT: E 307 HIS cc_start: 0.8283 (m90) cc_final: 0.8004 (m90) REVERT: E 423 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7927 (tt) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.0840 time to fit residues: 12.5178 Evaluate side-chains 94 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 330 GLN Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113732 restraints weight = 16036.163| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.96 r_work: 0.3395 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10646 Z= 0.134 Angle : 0.592 9.034 14896 Z= 0.338 Chirality : 0.041 0.221 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.979 166.590 2391 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 2.47 % Allowed : 18.82 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.27), residues: 956 helix: 1.25 (0.24), residues: 500 sheet: -0.92 (0.58), residues: 64 loop : -1.75 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 342 TYR 0.018 0.001 TYR E 241 PHE 0.015 0.001 PHE A 292 TRP 0.013 0.001 TRP A 41 HIS 0.002 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (10638) covalent geometry : angle 0.59168 / 0.34 (14892) hydrogen bonds : bond 0.04129 / 2.63 ( 520) hydrogen bonds : angle 4.16906 / 2.88 ( 1411) metal coordination : bond 0.00377 / 0.22 ( 8) metal coordination : angle 1.80222 / 0.80 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.215 Fit side-chains REVERT: A 145 SER cc_start: 0.8784 (p) cc_final: 0.8359 (m) REVERT: A 315 ASP cc_start: 0.8254 (m-30) cc_final: 0.7901 (m-30) REVERT: A 470 ASP cc_start: 0.8948 (t70) cc_final: 0.8703 (t70) REVERT: E 57 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6230 (pt0) REVERT: E 106 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7821 (mmt180) REVERT: E 173 MET cc_start: 0.7796 (mtp) cc_final: 0.7458 (mtp) REVERT: E 184 LYS cc_start: 0.8444 (tttt) cc_final: 0.7581 (tptp) REVERT: E 307 HIS cc_start: 0.8211 (m90) cc_final: 0.8000 (m90) REVERT: E 423 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7896 (tt) REVERT: E 470 ASP cc_start: 0.8325 (t70) cc_final: 0.8087 (t0) outliers start: 21 outliers final: 14 residues processed: 107 average time/residue: 0.0747 time to fit residues: 12.2176 Evaluate side-chains 92 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114260 restraints weight = 16265.563| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.96 r_work: 0.3414 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10646 Z= 0.132 Angle : 0.587 8.894 14896 Z= 0.335 Chirality : 0.041 0.226 1690 Planarity : 0.004 0.039 1452 Dihedral : 25.903 167.496 2391 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.47 % Allowed : 18.24 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 956 helix: 1.47 (0.24), residues: 500 sheet: -0.85 (0.57), residues: 64 loop : -1.64 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.018 0.001 TYR E 241 PHE 0.011 0.001 PHE A 180 TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (10638) covalent geometry : angle 0.58619 / 0.34 (14892) hydrogen bonds : bond 0.04003 / 2.54 ( 520) hydrogen bonds : angle 4.06054 / 2.81 ( 1411) metal coordination : bond 0.00415 / 0.24 ( 8) metal coordination : angle 1.63194 / 0.69 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.334 Fit side-chains REVERT: A 145 SER cc_start: 0.8768 (p) cc_final: 0.8357 (m) REVERT: A 219 MET cc_start: 0.8909 (ptm) cc_final: 0.8694 (ptm) REVERT: A 470 ASP cc_start: 0.8940 (t70) cc_final: 0.8702 (t70) REVERT: E 57 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6190 (pt0) REVERT: E 106 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7825 (mmt180) REVERT: E 173 MET cc_start: 0.7793 (mtp) cc_final: 0.7457 (mtp) REVERT: E 184 LYS cc_start: 0.8447 (tttt) cc_final: 0.7600 (tptp) REVERT: E 307 HIS cc_start: 0.8218 (m90) cc_final: 0.8006 (m90) REVERT: E 403 MET cc_start: 0.7858 (mtm) cc_final: 0.7631 (mtp) REVERT: E 423 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7857 (tt) REVERT: E 470 ASP cc_start: 0.8243 (t70) cc_final: 0.7881 (t0) outliers start: 21 outliers final: 17 residues processed: 105 average time/residue: 0.0825 time to fit residues: 13.3235 Evaluate side-chains 94 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.0370 chunk 61 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112568 restraints weight = 16030.325| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.04 r_work: 0.3397 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10646 Z= 0.146 Angle : 0.599 9.067 14896 Z= 0.339 Chirality : 0.041 0.238 1690 Planarity : 0.004 0.040 1452 Dihedral : 25.902 168.455 2391 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.35 % Allowed : 20.12 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 956 helix: 1.55 (0.24), residues: 502 sheet: -0.73 (0.58), residues: 64 loop : -1.67 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 437 TYR 0.017 0.001 TYR E 241 PHE 0.014 0.001 PHE A 292 TRP 0.011 0.001 TRP A 41 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (10638) covalent geometry : angle 0.59871 / 0.34 (14892) hydrogen bonds : bond 0.04076 / 2.59 ( 520) hydrogen bonds : angle 4.04384 / 2.80 ( 1411) metal coordination : bond 0.00533 / 0.30 ( 8) metal coordination : angle 1.52591 / 0.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 219 MET cc_start: 0.8969 (ptm) cc_final: 0.8741 (ptm) REVERT: E 106 ARG cc_start: 0.8054 (mmt180) cc_final: 0.7811 (mmt180) REVERT: E 173 MET cc_start: 0.7829 (mtp) cc_final: 0.7492 (mtp) REVERT: E 184 LYS cc_start: 0.8441 (tttt) cc_final: 0.7598 (tptp) REVERT: E 198 ASP cc_start: 0.8335 (m-30) cc_final: 0.8099 (m-30) REVERT: E 403 MET cc_start: 0.7925 (mtm) cc_final: 0.7683 (mtp) REVERT: E 423 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7870 (tt) REVERT: E 470 ASP cc_start: 0.8175 (t70) cc_final: 0.7916 (t0) outliers start: 20 outliers final: 18 residues processed: 98 average time/residue: 0.0882 time to fit residues: 13.1249 Evaluate side-chains 93 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.139921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114251 restraints weight = 16174.994| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.91 r_work: 0.3410 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10646 Z= 0.150 Angle : 0.597 9.439 14896 Z= 0.337 Chirality : 0.041 0.244 1690 Planarity : 0.004 0.040 1452 Dihedral : 25.904 169.029 2391 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.71 % Allowed : 20.12 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.28), residues: 956 helix: 1.64 (0.24), residues: 502 sheet: -0.66 (0.58), residues: 64 loop : -1.65 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 309 TYR 0.021 0.001 TYR E 241 PHE 0.012 0.001 PHE A 292 TRP 0.011 0.001 TRP A 41 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (10638) covalent geometry : angle 0.59641 / 0.34 (14892) hydrogen bonds : bond 0.04128 / 2.62 ( 520) hydrogen bonds : angle 4.02710 / 2.79 ( 1411) metal coordination : bond 0.00613 / 0.34 ( 8) metal coordination : angle 1.62531 / 0.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.343 Fit side-chains REVERT: A 124 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8810 (p90) REVERT: E 106 ARG cc_start: 0.8042 (mmt180) cc_final: 0.7783 (mmt180) REVERT: E 173 MET cc_start: 0.8056 (mtp) cc_final: 0.7699 (mtp) REVERT: E 184 LYS cc_start: 0.8520 (tttt) cc_final: 0.7688 (tppt) REVERT: E 198 ASP cc_start: 0.8452 (m-30) cc_final: 0.8219 (m-30) REVERT: E 403 MET cc_start: 0.8088 (mtm) cc_final: 0.7770 (mtp) REVERT: E 423 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7793 (tt) outliers start: 23 outliers final: 21 residues processed: 97 average time/residue: 0.0853 time to fit residues: 12.4685 Evaluate side-chains 97 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 40.0000 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107625 restraints weight = 16212.845| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.03 r_work: 0.3324 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 10646 Z= 0.256 Angle : 0.695 10.387 14896 Z= 0.379 Chirality : 0.045 0.266 1690 Planarity : 0.005 0.048 1452 Dihedral : 26.217 169.943 2391 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.94 % Allowed : 20.47 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 956 helix: 1.35 (0.24), residues: 500 sheet: -0.77 (0.60), residues: 64 loop : -1.64 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 52 TYR 0.020 0.002 TYR E 73 PHE 0.013 0.002 PHE A 292 TRP 0.010 0.002 TRP A 41 HIS 0.006 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.26 (10638) covalent geometry : angle 0.69352 / 0.38 (14892) hydrogen bonds : bond 0.04998 / 3.17 ( 520) hydrogen bonds : angle 4.27615 / 2.95 ( 1411) metal coordination : bond 0.01469 / 0.85 ( 8) metal coordination : angle 2.35945 / 0.99 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.448 Fit side-chains REVERT: A 124 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.9111 (p90) REVERT: E 106 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7786 (mmt180) REVERT: E 173 MET cc_start: 0.7888 (mtp) cc_final: 0.7570 (mtp) REVERT: E 184 LYS cc_start: 0.8478 (tttt) cc_final: 0.7715 (tppt) REVERT: E 198 ASP cc_start: 0.8406 (m-30) cc_final: 0.8139 (m-30) REVERT: E 403 MET cc_start: 0.7946 (mtm) cc_final: 0.7729 (mtp) outliers start: 25 outliers final: 20 residues processed: 94 average time/residue: 0.0844 time to fit residues: 12.1395 Evaluate side-chains 86 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111433 restraints weight = 15964.847| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.01 r_work: 0.3381 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10646 Z= 0.145 Angle : 0.617 11.343 14896 Z= 0.349 Chirality : 0.042 0.243 1690 Planarity : 0.004 0.040 1452 Dihedral : 26.016 169.754 2389 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.35 % Allowed : 21.06 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 956 helix: 1.55 (0.24), residues: 500 sheet: -0.87 (0.59), residues: 64 loop : -1.54 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 343 TYR 0.020 0.001 TYR E 241 PHE 0.015 0.001 PHE A 344 TRP 0.016 0.001 TRP A 41 HIS 0.002 0.000 HIS E 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (10638) covalent geometry : angle 0.61628 / 0.35 (14892) hydrogen bonds : bond 0.04288 / 2.73 ( 520) hydrogen bonds : angle 4.13948 / 2.88 ( 1411) metal coordination : bond 0.00567 / 0.34 ( 8) metal coordination : angle 1.27721 / 0.58 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.368 Fit side-chains REVERT: A 124 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8990 (p90) REVERT: E 56 LYS cc_start: 0.6979 (pttt) cc_final: 0.6778 (pttm) REVERT: E 106 ARG cc_start: 0.8031 (mmt180) cc_final: 0.7775 (mmt180) REVERT: E 173 MET cc_start: 0.7862 (mtp) cc_final: 0.7530 (mtp) REVERT: E 184 LYS cc_start: 0.8440 (tttt) cc_final: 0.7629 (tppt) REVERT: E 198 ASP cc_start: 0.8392 (m-30) cc_final: 0.8150 (m-30) REVERT: E 403 MET cc_start: 0.7885 (mtm) cc_final: 0.7648 (mtp) outliers start: 20 outliers final: 17 residues processed: 94 average time/residue: 0.0849 time to fit residues: 12.2280 Evaluate side-chains 91 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 487 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 96 optimal weight: 40.0000 chunk 1 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.113371 restraints weight = 16010.045| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.96 r_work: 0.3394 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10646 Z= 0.151 Angle : 0.612 11.091 14896 Z= 0.346 Chirality : 0.042 0.257 1690 Planarity : 0.004 0.041 1452 Dihedral : 25.948 170.015 2389 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.35 % Allowed : 20.82 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.28), residues: 956 helix: 1.63 (0.24), residues: 502 sheet: -0.81 (0.59), residues: 64 loop : -1.63 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 52 TYR 0.019 0.001 TYR E 241 PHE 0.015 0.002 PHE A 347 TRP 0.012 0.001 TRP A 41 HIS 0.002 0.001 HIS E 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (10638) covalent geometry : angle 0.61173 / 0.35 (14892) hydrogen bonds : bond 0.04255 / 2.70 ( 520) hydrogen bonds : angle 4.10005 / 2.86 ( 1411) metal coordination : bond 0.00690 / 0.41 ( 8) metal coordination : angle 1.27371 / 0.55 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.79 seconds wall clock time: 35 minutes 43.37 seconds (2143.37 seconds total)