Starting phenix.real_space_refine on Tue Mar 3 23:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pqr_20452/03_2026/6pqr_20452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqr_20452/03_2026/6pqr_20452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2026/6pqr_20452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2026/6pqr_20452.map" model { file = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2026/6pqr_20452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqr_20452/03_2026/6pqr_20452.cif" } resolution = 3.4 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 2 6.06 5 P 88 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5612 2.51 5 N 1592 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9266 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3728 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 1, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1629 SG CYS A 240 77.598 110.856 39.273 1.00166.71 S ATOM 1655 SG CYS A 243 80.541 111.292 41.321 1.00170.90 S ATOM 6259 SG CYS D 240 25.377 15.136 39.255 1.00167.58 S ATOM 6285 SG CYS D 243 22.435 14.693 41.303 1.00171.67 S Time building chain proxies: 2.21, per 1000 atoms: 0.24 Number of scatterers: 9266 At special positions: 0 Unit cell: (103.95, 127.05, 91.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 2 19.00 S 34 16.00 P 88 15.00 Mg 2 11.99 O 1934 8.00 N 1592 7.00 C 5612 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: 0.84 Conformation dependent library (CDL) restraints added in 296.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 413 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 408 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 243 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 240 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 413 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 408 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 243 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 240 " Number of angles added : 4 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 51.7% alpha, 15.8% beta 34 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.619A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.621A pdb=" N THR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.618A pdb=" N GLN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.069A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.547A pdb=" N VAL A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 289 removed outlier: 3.885A pdb=" N MET A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 321 Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.507A pdb=" N ARG A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.621A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 removed outlier: 3.522A pdb=" N GLU A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.585A pdb=" N LEU A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.868A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.735A pdb=" N ILE A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.797A pdb=" N VAL A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 494' Processing helix chain 'D' and resid 25 through 36 removed outlier: 3.619A pdb=" N LEU D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.623A pdb=" N THR D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.612A pdb=" N GLN D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 105 Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.070A pdb=" N TYR D 174 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.547A pdb=" N VAL D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 276 through 289 removed outlier: 3.884A pdb=" N MET D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 321 Processing helix chain 'D' and resid 337 through 347 removed outlier: 4.507A pdb=" N ARG D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 358 through 373 removed outlier: 3.620A pdb=" N ILE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 396 removed outlier: 3.522A pdb=" N GLU D 385 " --> pdb=" O PRO D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.585A pdb=" N LEU D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.868A pdb=" N ILE D 417 " --> pdb=" O HIS D 413 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 447 Processing helix chain 'D' and resid 453 through 468 removed outlier: 3.734A pdb=" N ILE D 467 " --> pdb=" O ASN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 494 removed outlier: 3.796A pdb=" N VAL D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 494' Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 151 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 165 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 156 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 151 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 179 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE A 147 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA A 127 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR A 149 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP A 125 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 151 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY A 123 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A 121 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N LEU A 116 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N LEU A 218 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LEU A 118 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N MET A 220 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N SER A 120 " --> pdb=" O MET A 220 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N MET A 222 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP A 122 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.261A pdb=" N ILE A 377 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL D 178 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 151 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 179 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU D 154 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL D 165 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 156 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.228A pdb=" N VAL D 178 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU D 151 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 179 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE D 147 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA D 127 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR D 149 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP D 125 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 151 " --> pdb=" O GLY D 123 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY D 123 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 121 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N LEU D 116 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N LEU D 218 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N LEU D 118 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N MET D 220 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 10.751A pdb=" N SER D 120 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N MET D 222 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP D 122 " --> pdb=" O MET D 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 378 removed outlier: 4.261A pdb=" N ILE D 377 " --> pdb=" O GLN D 497 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.09 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: 2078 1.33 - 1.45: 2347 1.45 - 1.57: 4965 1.57 - 1.69: 172 1.69 - 1.81: 52 Bond restraints: 9614 Sorted by residual: bond pdb=" CG ARG A 450 " pdb=" CD ARG A 450 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" CG ARG D 450 " pdb=" CD ARG D 450 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.80e+00 bond pdb=" CA PHE D 147 " pdb=" CB PHE D 147 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.53e-02 4.27e+03 3.70e+00 bond pdb=" CA PHE A 147 " pdb=" CB PHE A 147 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.53e-02 4.27e+03 3.59e+00 bond pdb=" CB ARG D 450 " pdb=" CG ARG D 450 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 ... (remaining 9609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12178 1.37 - 2.74: 1003 2.74 - 4.11: 127 4.11 - 5.48: 38 5.48 - 6.84: 8 Bond angle restraints: 13354 Sorted by residual: angle pdb=" C GLU D 103 " pdb=" N THR D 104 " pdb=" CA THR D 104 " ideal model delta sigma weight residual 122.24 115.40 6.84 1.57e+00 4.06e-01 1.90e+01 angle pdb=" C GLU A 103 " pdb=" N THR A 104 " pdb=" CA THR A 104 " ideal model delta sigma weight residual 122.24 115.43 6.81 1.57e+00 4.06e-01 1.88e+01 angle pdb=" C GLU D 502 " pdb=" N ALA D 503 " pdb=" CA ALA D 503 " ideal model delta sigma weight residual 122.59 117.91 4.68 1.11e+00 8.12e-01 1.78e+01 angle pdb=" C GLU A 502 " pdb=" N ALA A 503 " pdb=" CA ALA A 503 " ideal model delta sigma weight residual 122.59 117.94 4.65 1.11e+00 8.12e-01 1.75e+01 angle pdb=" C ALA D 234 " pdb=" N LYS D 235 " pdb=" CA LYS D 235 " ideal model delta sigma weight residual 120.82 126.88 -6.06 1.50e+00 4.44e-01 1.63e+01 ... (remaining 13349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 4336 16.84 - 33.68: 716 33.68 - 50.52: 394 50.52 - 67.37: 154 67.37 - 84.21: 14 Dihedral angle restraints: 5614 sinusoidal: 2862 harmonic: 2752 Sorted by residual: dihedral pdb=" CA ASP D 326 " pdb=" C ASP D 326 " pdb=" N ILE D 327 " pdb=" CA ILE D 327 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASP A 326 " pdb=" C ASP A 326 " pdb=" N ILE A 327 " pdb=" CA ILE A 327 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA A 234 " pdb=" C ALA A 234 " pdb=" N LYS A 235 " pdb=" CA LYS A 235 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 5611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 869 0.037 - 0.075: 487 0.075 - 0.112: 126 0.112 - 0.149: 27 0.149 - 0.186: 13 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB ILE D 105 " pdb=" CA ILE D 105 " pdb=" CG1 ILE D 105 " pdb=" CG2 ILE D 105 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 1519 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 450 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ARG D 450 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG D 450 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS D 451 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 450 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ARG A 450 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG A 450 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 451 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 31 " -0.019 2.00e-02 2.50e+03 8.23e-03 1.86e+00 pdb=" N9 DA B 31 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA B 31 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA B 31 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA B 31 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA B 31 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA B 31 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA B 31 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA B 31 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA B 31 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA B 31 " 0.007 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 462 2.69 - 3.30: 10606 3.30 - 3.92: 18688 3.92 - 4.53: 24093 4.53 - 5.14: 36038 Nonbonded interactions: 89887 Sorted by model distance: nonbonded pdb=" OD1 ASP A 125 " pdb="MG MG A 601 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP D 125 " pdb="MG MG D 601 " model vdw 2.081 2.170 nonbonded pdb=" OD2 ASP A 224 " pdb="MG MG A 601 " model vdw 2.098 2.170 nonbonded pdb=" OD2 ASP D 224 " pdb="MG MG D 601 " model vdw 2.098 2.170 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASP D 188 " model vdw 2.201 3.040 ... (remaining 89882 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' 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=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: 1.020 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.060 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.009 0.059 9622 Z= 0.410 Angle : 0.857 13.236 13358 Z= 0.506 Chirality : 0.049 0.186 1522 Planarity : 0.004 0.033 1380 Dihedral : 22.102 84.207 3822 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.24 % Allowed : 11.59 % Favored : 88.16 % 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: -3.38 (0.23), residues: 920 helix: -2.20 (0.19), residues: 452 sheet: -0.96 (0.57), residues: 60 loop : -2.38 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 450 TYR 0.011 0.002 TYR A 394 PHE 0.023 0.002 PHE A 102 TRP 0.016 0.003 TRP A 400 HIS 0.008 0.002 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00903 ( 9614) covalent geometry : angle 0.83906 (13354) hydrogen bonds : bond 0.14442 ( 420) hydrogen bonds : angle 6.83112 ( 1198) metal coordination : bond 0.03271 ( 8) metal coordination : angle 10.25246 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 HIS cc_start: 0.7547 (m90) cc_final: 0.7150 (m170) REVERT: A 344 PHE cc_start: 0.7881 (t80) cc_final: 0.7551 (t80) REVERT: A 417 ILE cc_start: 0.7852 (mm) cc_final: 0.7599 (mt) REVERT: D 285 HIS cc_start: 0.7553 (m90) cc_final: 0.7164 (m170) REVERT: D 344 PHE cc_start: 0.7873 (t80) cc_final: 0.7467 (t80) outliers start: 2 outliers final: 2 residues processed: 115 average time/residue: 0.1097 time to fit residues: 17.4198 Evaluate side-chains 80 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 314 GLN A 421 ASN A 448 HIS D 314 GLN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN D 448 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.185265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.130409 restraints weight = 14171.009| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.90 r_work: 0.3628 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9622 Z= 0.139 Angle : 0.613 7.410 13358 Z= 0.340 Chirality : 0.042 0.202 1522 Planarity : 0.004 0.048 1380 Dihedral : 24.936 70.767 1972 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.45 % Allowed : 16.06 % Favored : 82.49 % 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: -1.90 (0.25), residues: 920 helix: -0.84 (0.22), residues: 442 sheet: -0.26 (0.60), residues: 60 loop : -1.83 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 343 TYR 0.012 0.002 TYR D 241 PHE 0.013 0.002 PHE D 268 TRP 0.007 0.001 TRP A 41 HIS 0.005 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9614) covalent geometry : angle 0.61142 (13354) hydrogen bonds : bond 0.03888 ( 420) hydrogen bonds : angle 4.48231 ( 1198) metal coordination : bond 0.00506 ( 8) metal coordination : angle 2.76079 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7826 (ttp) cc_final: 0.7265 (ttp) REVERT: A 281 GLU cc_start: 0.7715 (pp20) cc_final: 0.7486 (pp20) REVERT: A 285 HIS cc_start: 0.7962 (m90) cc_final: 0.7507 (m-70) REVERT: A 344 PHE cc_start: 0.7840 (t80) cc_final: 0.7592 (t80) REVERT: A 364 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7260 (ptm160) REVERT: D 281 GLU cc_start: 0.7759 (pp20) cc_final: 0.7523 (pp20) REVERT: D 285 HIS cc_start: 0.7956 (m90) cc_final: 0.7554 (m-70) outliers start: 12 outliers final: 5 residues processed: 118 average time/residue: 0.0942 time to fit residues: 16.0845 Evaluate side-chains 97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 94 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 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 = 0.4492 r_free = 0.4492 target = 0.190702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.137703 restraints weight = 14210.647| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.79 r_work: 0.3649 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9622 Z= 0.145 Angle : 0.575 8.566 13358 Z= 0.317 Chirality : 0.041 0.225 1522 Planarity : 0.004 0.032 1380 Dihedral : 24.681 68.293 1972 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.69 % Allowed : 17.87 % Favored : 80.43 % 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: -1.43 (0.26), residues: 920 helix: -0.36 (0.22), residues: 444 sheet: 0.03 (0.63), residues: 60 loop : -1.71 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 342 TYR 0.010 0.001 TYR D 488 PHE 0.010 0.002 PHE A 268 TRP 0.007 0.001 TRP D 400 HIS 0.003 0.001 HIS D 413 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9614) covalent geometry : angle 0.57244 (13354) hydrogen bonds : bond 0.03568 ( 420) hydrogen bonds : angle 4.11689 ( 1198) metal coordination : bond 0.00374 ( 8) metal coordination : angle 2.94012 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7764 (ttp) cc_final: 0.7197 (ttp) REVERT: A 285 HIS cc_start: 0.7953 (m90) cc_final: 0.7702 (m170) REVERT: D 281 GLU cc_start: 0.7678 (pp20) cc_final: 0.7420 (pp20) REVERT: D 285 HIS cc_start: 0.7899 (m90) cc_final: 0.7363 (m-70) REVERT: D 344 PHE cc_start: 0.8123 (t80) cc_final: 0.7837 (t80) outliers start: 14 outliers final: 8 residues processed: 116 average time/residue: 0.0837 time to fit residues: 14.3011 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 492 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS D 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.191671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139273 restraints weight = 14351.296| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.73 r_work: 0.3670 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.003 0.046 9622 Z= 0.137 Angle : 0.570 8.580 13358 Z= 0.313 Chirality : 0.040 0.223 1522 Planarity : 0.003 0.030 1380 Dihedral : 24.533 66.171 1972 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.69 % Allowed : 19.20 % Favored : 79.11 % 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: -1.09 (0.26), residues: 920 helix: -0.03 (0.23), residues: 446 sheet: 0.20 (0.65), residues: 60 loop : -1.62 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 106 TYR 0.014 0.001 TYR A 488 PHE 0.015 0.002 PHE D 345 TRP 0.007 0.001 TRP A 164 HIS 0.002 0.001 HIS D 413 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9614) covalent geometry : angle 0.56835 (13354) hydrogen bonds : bond 0.03331 ( 420) hydrogen bonds : angle 4.01549 ( 1198) metal coordination : bond 0.00590 ( 8) metal coordination : angle 2.24597 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 MET cc_start: 0.7767 (ttp) cc_final: 0.7425 (ttp) REVERT: A 281 GLU cc_start: 0.7783 (pp20) cc_final: 0.7563 (tm-30) REVERT: A 344 PHE cc_start: 0.8159 (t80) cc_final: 0.7712 (t80) REVERT: D 226 LYS cc_start: 0.8295 (ptpt) cc_final: 0.8018 (mttm) REVERT: D 280 MET cc_start: 0.6786 (ttp) cc_final: 0.5906 (tpt) REVERT: D 285 HIS cc_start: 0.7956 (m90) cc_final: 0.7673 (m170) REVERT: D 344 PHE cc_start: 0.8069 (t80) cc_final: 0.7845 (t80) outliers start: 14 outliers final: 7 residues processed: 100 average time/residue: 0.0765 time to fit residues: 11.4530 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 0.0060 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.192557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139904 restraints weight = 14521.193| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.73 r_work: 0.3676 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9622 Z= 0.137 Angle : 0.548 7.829 13358 Z= 0.302 Chirality : 0.039 0.194 1522 Planarity : 0.003 0.030 1380 Dihedral : 24.424 64.091 1972 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.66 % Allowed : 18.84 % Favored : 78.50 % 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: -0.92 (0.26), residues: 920 helix: 0.21 (0.23), residues: 448 sheet: 0.36 (0.66), residues: 60 loop : -1.68 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 106 TYR 0.007 0.001 TYR A 488 PHE 0.012 0.001 PHE D 489 TRP 0.006 0.001 TRP D 400 HIS 0.002 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9614) covalent geometry : angle 0.54787 (13354) hydrogen bonds : bond 0.03245 ( 420) hydrogen bonds : angle 3.81559 ( 1198) metal coordination : bond 0.00568 ( 8) metal coordination : angle 1.52277 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8282 (ptpt) cc_final: 0.8028 (mttm) REVERT: A 280 MET cc_start: 0.7796 (ttp) cc_final: 0.6750 (tpt) REVERT: A 402 TYR cc_start: 0.6118 (m-80) cc_final: 0.5379 (p90) REVERT: D 226 LYS cc_start: 0.8301 (ptpt) cc_final: 0.8057 (mttm) REVERT: D 285 HIS cc_start: 0.7997 (m90) cc_final: 0.7789 (m170) REVERT: D 344 PHE cc_start: 0.8008 (t80) cc_final: 0.7748 (t80) REVERT: D 392 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7506 (mt-10) outliers start: 22 outliers final: 9 residues processed: 108 average time/residue: 0.0831 time to fit residues: 13.3372 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ARG Chi-restraints excluded: chain D residue 171 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.193980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.141456 restraints weight = 14472.272| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.78 r_work: 0.3699 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9622 Z= 0.123 Angle : 0.531 5.991 13358 Z= 0.293 Chirality : 0.038 0.158 1522 Planarity : 0.003 0.031 1380 Dihedral : 24.255 67.267 1972 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.57 % Allowed : 20.05 % Favored : 78.38 % 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: -0.77 (0.26), residues: 920 helix: 0.35 (0.23), residues: 448 sheet: 0.62 (0.68), residues: 60 loop : -1.67 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 106 TYR 0.020 0.001 TYR D 488 PHE 0.012 0.001 PHE D 489 TRP 0.005 0.001 TRP A 400 HIS 0.003 0.001 HIS D 413 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9614) covalent geometry : angle 0.53022 (13354) hydrogen bonds : bond 0.03130 ( 420) hydrogen bonds : angle 3.71420 ( 1198) metal coordination : bond 0.00310 ( 8) metal coordination : angle 1.57877 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8317 (ptpt) cc_final: 0.8102 (mttm) REVERT: A 280 MET cc_start: 0.7648 (ttp) cc_final: 0.6987 (tpt) REVERT: A 357 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6489 (mm) REVERT: A 402 TYR cc_start: 0.6246 (m-80) cc_final: 0.5538 (p90) REVERT: A 403 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6462 (tpp) REVERT: D 226 LYS cc_start: 0.8304 (ptpt) cc_final: 0.8035 (mttm) REVERT: D 284 LEU cc_start: 0.7397 (mt) cc_final: 0.7071 (mt) REVERT: D 285 HIS cc_start: 0.7924 (m90) cc_final: 0.7666 (m170) REVERT: D 344 PHE cc_start: 0.7878 (t80) cc_final: 0.7665 (t80) REVERT: D 357 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6459 (mm) outliers start: 13 outliers final: 5 residues processed: 103 average time/residue: 0.0834 time to fit residues: 12.7322 Evaluate side-chains 101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 0.0040 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.194621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141978 restraints weight = 14414.713| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.80 r_work: 0.3710 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9622 Z= 0.121 Angle : 0.530 6.031 13358 Z= 0.292 Chirality : 0.038 0.162 1522 Planarity : 0.003 0.028 1380 Dihedral : 24.121 69.197 1970 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.29 % Allowed : 19.69 % Favored : 78.02 % 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: -0.69 (0.26), residues: 920 helix: 0.46 (0.23), residues: 448 sheet: 0.74 (0.66), residues: 64 loop : -1.72 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 106 TYR 0.015 0.001 TYR A 488 PHE 0.013 0.001 PHE A 489 TRP 0.005 0.001 TRP D 400 HIS 0.002 0.000 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9614) covalent geometry : angle 0.52866 (13354) hydrogen bonds : bond 0.03124 ( 420) hydrogen bonds : angle 3.63051 ( 1198) metal coordination : bond 0.00432 ( 8) metal coordination : angle 1.82349 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.3234 (OUTLIER) cc_final: 0.2843 (pt) REVERT: A 280 MET cc_start: 0.7593 (ttp) cc_final: 0.7071 (tpt) REVERT: A 357 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6461 (mm) REVERT: A 402 TYR cc_start: 0.6419 (m-80) cc_final: 0.5631 (p90) REVERT: A 403 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5983 (tpp) REVERT: D 226 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7976 (mttm) REVERT: D 261 ILE cc_start: 0.3250 (OUTLIER) cc_final: 0.2857 (pt) REVERT: D 284 LEU cc_start: 0.7409 (mt) cc_final: 0.7097 (mt) REVERT: D 285 HIS cc_start: 0.7948 (m90) cc_final: 0.7698 (m170) REVERT: D 357 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6448 (mm) REVERT: D 402 TYR cc_start: 0.6151 (m-80) cc_final: 0.5497 (p90) outliers start: 19 outliers final: 7 residues processed: 103 average time/residue: 0.0830 time to fit residues: 12.5682 Evaluate side-chains 100 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.190365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.134955 restraints weight = 14418.278| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.97 r_work: 0.3694 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9622 Z= 0.125 Angle : 0.528 6.001 13358 Z= 0.291 Chirality : 0.037 0.157 1522 Planarity : 0.003 0.030 1380 Dihedral : 23.997 71.252 1970 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.69 % Allowed : 20.29 % Favored : 78.02 % 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: -0.65 (0.27), residues: 920 helix: 0.42 (0.23), residues: 462 sheet: 0.87 (0.66), residues: 64 loop : -1.69 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 106 TYR 0.013 0.001 TYR D 488 PHE 0.013 0.001 PHE D 489 TRP 0.013 0.001 TRP D 122 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9614) covalent geometry : angle 0.52776 (13354) hydrogen bonds : bond 0.03099 ( 420) hydrogen bonds : angle 3.62201 ( 1198) metal coordination : bond 0.00437 ( 8) metal coordination : angle 0.91702 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.3271 (OUTLIER) cc_final: 0.2916 (pt) REVERT: A 280 MET cc_start: 0.7559 (ttp) cc_final: 0.7030 (tpt) REVERT: A 357 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6485 (mm) REVERT: A 402 TYR cc_start: 0.6412 (m-80) cc_final: 0.5623 (p90) REVERT: A 403 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6183 (tpp) REVERT: D 261 ILE cc_start: 0.3286 (OUTLIER) cc_final: 0.2883 (pt) REVERT: D 284 LEU cc_start: 0.7412 (mt) cc_final: 0.7153 (mt) REVERT: D 285 HIS cc_start: 0.8066 (m90) cc_final: 0.7830 (m170) REVERT: D 357 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6503 (mm) REVERT: D 402 TYR cc_start: 0.6314 (m-80) cc_final: 0.5581 (p90) outliers start: 14 outliers final: 7 residues processed: 90 average time/residue: 0.0871 time to fit residues: 11.6324 Evaluate side-chains 94 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 29 optimal weight: 0.0070 chunk 82 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.191126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.135783 restraints weight = 14635.666| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.93 r_work: 0.3667 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9622 Z= 0.146 Angle : 0.542 5.948 13358 Z= 0.297 Chirality : 0.038 0.162 1522 Planarity : 0.003 0.028 1380 Dihedral : 23.957 72.932 1970 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.69 % Allowed : 20.29 % Favored : 78.02 % 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: -0.64 (0.27), residues: 920 helix: 0.42 (0.23), residues: 464 sheet: 0.81 (0.67), residues: 64 loop : -1.68 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 106 TYR 0.013 0.001 TYR D 488 PHE 0.013 0.001 PHE D 345 TRP 0.006 0.001 TRP D 400 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9614) covalent geometry : angle 0.54173 (13354) hydrogen bonds : bond 0.03215 ( 420) hydrogen bonds : angle 3.62192 ( 1198) metal coordination : bond 0.00606 ( 8) metal coordination : angle 0.60557 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 261 ILE cc_start: 0.3413 (OUTLIER) cc_final: 0.3014 (pt) REVERT: A 280 MET cc_start: 0.7578 (ttp) cc_final: 0.6989 (tpt) REVERT: A 357 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6465 (mm) REVERT: A 364 ARG cc_start: 0.7521 (mtt90) cc_final: 0.7269 (ptm160) REVERT: A 392 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 402 TYR cc_start: 0.6421 (m-80) cc_final: 0.5653 (p90) REVERT: A 403 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6043 (tpp) REVERT: D 261 ILE cc_start: 0.3372 (OUTLIER) cc_final: 0.2969 (pt) REVERT: D 280 MET cc_start: 0.6990 (ttp) cc_final: 0.6430 (tpt) REVERT: D 285 HIS cc_start: 0.8041 (m90) cc_final: 0.7822 (m170) REVERT: D 357 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6574 (mm) REVERT: D 392 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7315 (mt-10) REVERT: D 402 TYR cc_start: 0.6339 (m-80) cc_final: 0.5599 (p90) REVERT: D 403 MET cc_start: 0.6234 (tpp) cc_final: 0.5653 (tpp) outliers start: 14 outliers final: 7 residues processed: 93 average time/residue: 0.0840 time to fit residues: 11.7005 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.195345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.140815 restraints weight = 14788.488| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.92 r_work: 0.3688 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9622 Z= 0.136 Angle : 0.535 5.892 13358 Z= 0.296 Chirality : 0.038 0.158 1522 Planarity : 0.003 0.030 1380 Dihedral : 23.860 75.772 1970 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.57 % Allowed : 21.01 % Favored : 77.42 % 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: -0.52 (0.27), residues: 920 helix: 0.53 (0.23), residues: 462 sheet: 0.89 (0.67), residues: 64 loop : -1.63 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 106 TYR 0.012 0.001 TYR D 488 PHE 0.013 0.001 PHE D 489 TRP 0.007 0.001 TRP A 122 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9614) covalent geometry : angle 0.53496 (13354) hydrogen bonds : bond 0.03142 ( 420) hydrogen bonds : angle 3.60590 ( 1198) metal coordination : bond 0.00455 ( 8) metal coordination : angle 0.62030 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 261 ILE cc_start: 0.3493 (OUTLIER) cc_final: 0.3088 (pt) REVERT: A 280 MET cc_start: 0.7580 (ttp) cc_final: 0.6989 (tpt) REVERT: A 357 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6507 (mm) REVERT: A 364 ARG cc_start: 0.7513 (mtt90) cc_final: 0.7272 (ptm160) REVERT: A 392 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7194 (mt-10) REVERT: A 402 TYR cc_start: 0.6380 (m-80) cc_final: 0.5593 (p90) REVERT: A 403 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6281 (tpp) REVERT: D 261 ILE cc_start: 0.3384 (OUTLIER) cc_final: 0.2970 (pt) REVERT: D 280 MET cc_start: 0.7130 (ttp) cc_final: 0.6466 (tpt) REVERT: D 357 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6687 (mm) REVERT: D 392 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7308 (mt-10) REVERT: D 402 TYR cc_start: 0.6386 (m-80) cc_final: 0.5511 (p90) REVERT: D 403 MET cc_start: 0.5960 (tpp) cc_final: 0.5397 (tpp) outliers start: 13 outliers final: 5 residues processed: 96 average time/residue: 0.0827 time to fit residues: 12.0125 Evaluate side-chains 97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 0.0030 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.195079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.142692 restraints weight = 14255.276| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.76 r_work: 0.3710 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9622 Z= 0.132 Angle : 0.537 7.560 13358 Z= 0.297 Chirality : 0.038 0.160 1522 Planarity : 0.003 0.030 1380 Dihedral : 23.815 76.968 1970 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.21 % Allowed : 21.38 % Favored : 77.42 % 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: -0.47 (0.27), residues: 920 helix: 0.56 (0.23), residues: 462 sheet: 1.03 (0.67), residues: 64 loop : -1.62 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 106 TYR 0.010 0.001 TYR D 488 PHE 0.014 0.001 PHE A 489 TRP 0.009 0.001 TRP A 164 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9614) covalent geometry : angle 0.53715 (13354) hydrogen bonds : bond 0.03115 ( 420) hydrogen bonds : angle 3.59633 ( 1198) metal coordination : bond 0.00250 ( 8) metal coordination : angle 0.78280 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.63 seconds wall clock time: 39 minutes 21.65 seconds (2361.65 seconds total)