Starting phenix.real_space_refine on Wed Aug 5 13:46:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22bu_68158/08_2026/22bu_68158.cif Found real_map, /net/cci-nas-00/data/ceres_data/22bu_68158/08_2026/22bu_68158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22bu_68158/08_2026/22bu_68158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22bu_68158/08_2026/22bu_68158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22bu_68158/08_2026/22bu_68158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22bu_68158/08_2026/22bu_68158.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2 5.49 5 S 31 5.16 5 C 6190 2.51 5 N 1726 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9815 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4021 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4045 Classifications: {'peptide': 500} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 482} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1721 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8416 SG CYS F 43 64.986 50.777 86.963 1.00149.26 S ATOM 8439 SG CYS F 46 65.905 53.644 85.112 1.00108.34 S ATOM 8696 SG CYS F 78 65.692 49.920 83.509 1.00121.59 S ATOM 8780 SG CYS F 90 68.716 51.669 84.075 1.00125.49 S Time building chain proxies: 2.47, per 1000 atoms: 0.25 Number of scatterers: 9815 At special positions: 0 Unit cell: (107.52, 108.48, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 2 15.00 O 1865 8.00 N 1726 7.00 C 6190 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: 0.87 Conformation dependent library (CDL) restraints added in 227.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " Number of angles added : 6 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 53.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 1 through 12 removed outlier: 3.655A pdb=" N LEU B 5 " --> pdb=" O VAL B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 removed outlier: 4.472A pdb=" N ASN B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 Processing helix chain 'B' and resid 98 through 120 removed outlier: 3.639A pdb=" N SER B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.680A pdb=" N ARG B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 239 through 256 removed outlier: 3.886A pdb=" N ALA B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 359 through 380 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.512A pdb=" N GLY B 389 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 409 through 418 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 435 through 436 No H-bonds generated for 'chain 'B' and resid 435 through 436' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 484 through 487 Processing helix chain 'B' and resid 488 through 498 Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 523 through 551 removed outlier: 3.511A pdb=" N LYS B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 13 through 28 Processing helix chain 'C' and resid 33 through 48 Processing helix chain 'C' and resid 99 through 120 removed outlier: 3.733A pdb=" N LEU C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 194 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 239 through 256 removed outlier: 3.521A pdb=" N ALA C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 359 through 380 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.605A pdb=" N GLY C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 removed outlier: 4.029A pdb=" N GLU C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.550A pdb=" N LEU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 436 No H-bonds generated for 'chain 'C' and resid 435 through 436' Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 484 through 487 Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 505 through 519 Processing helix chain 'C' and resid 523 through 551 Processing helix chain 'F' and resid 10 through 16 removed outlier: 4.155A pdb=" N HIS F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE F 16 " --> pdb=" O HIS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 26 removed outlier: 3.632A pdb=" N SER F 25 " --> pdb=" O PRO F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 40 removed outlier: 3.941A pdb=" N ILE F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 90 through 97 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 113 through 116 Processing helix chain 'F' and resid 134 through 148 Processing helix chain 'F' and resid 152 through 181 removed outlier: 4.431A pdb=" N GLU F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU F 169 " --> pdb=" O TYR F 165 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.540A pdb=" N TRP F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 84 removed outlier: 6.358A pdb=" N GLN B 80 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 73 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP B 82 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 71 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 84 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 69 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU B 67 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 150 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 69 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 144 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE B 75 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N PHE B 142 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N PHE B 151 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 200 through 204 removed outlier: 6.150A pdb=" N THR B 90 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG B 442 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 91 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE B 444 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE B 93 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N GLN B 446 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 330 through 336 removed outlier: 4.074A pdb=" N ARG B 332 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 84 removed outlier: 5.374A pdb=" N LEU C 67 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C 150 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 69 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP C 144 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE C 75 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N PHE C 142 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE C 151 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 200 through 204 removed outlier: 6.554A pdb=" N GLY C 391 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL C 424 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 393 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N THR C 426 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE C 395 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ARG C 442 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 91 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE C 444 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE C 93 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLN C 446 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 330 through 336 removed outlier: 4.426A pdb=" N ARG C 332 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AA8, first strand: chain 'F' and resid 118 through 120 489 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3296 1.34 - 1.46: 1970 1.46 - 1.58: 4698 1.58 - 1.69: 3 1.69 - 1.81: 51 Bond restraints: 10018 Sorted by residual: bond pdb=" CB ASP C 122 " pdb=" CG ASP C 122 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.24e+00 bond pdb=" C HIS C 210 " pdb=" N PRO C 211 " ideal model delta sigma weight residual 1.333 1.348 -0.014 1.01e-02 9.80e+03 1.98e+00 bond pdb=" CA GLN C 351 " pdb=" CB GLN C 351 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.43e-02 4.89e+03 1.45e+00 bond pdb=" CB GLU B 255 " pdb=" CG GLU B 255 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB ASN F 198 " pdb=" CG ASN F 198 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 ... (remaining 10013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 13395 2.47 - 4.95: 128 4.95 - 7.42: 16 7.42 - 9.90: 4 9.90 - 12.37: 1 Bond angle restraints: 13544 Sorted by residual: angle pdb=" CA LEU B 42 " pdb=" CB LEU B 42 " pdb=" CG LEU B 42 " ideal model delta sigma weight residual 116.30 128.67 -12.37 3.50e+00 8.16e-02 1.25e+01 angle pdb=" CA GLY F 181 " pdb=" C GLY F 181 " pdb=" O GLY F 181 " ideal model delta sigma weight residual 122.45 119.99 2.46 7.20e-01 1.93e+00 1.17e+01 angle pdb=" CB MET F 24 " pdb=" CG MET F 24 " pdb=" SD MET F 24 " ideal model delta sigma weight residual 112.70 122.24 -9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CA GLN F 15 " pdb=" CB GLN F 15 " pdb=" CG GLN F 15 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.62e+00 angle pdb=" CA GLU B 255 " pdb=" CB GLU B 255 " pdb=" CG GLU B 255 " ideal model delta sigma weight residual 114.10 119.96 -5.86 2.00e+00 2.50e-01 8.59e+00 ... (remaining 13539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5149 17.90 - 35.81: 680 35.81 - 53.71: 192 53.71 - 71.61: 32 71.61 - 89.52: 16 Dihedral angle restraints: 6069 sinusoidal: 2524 harmonic: 3545 Sorted by residual: dihedral pdb=" CA SER C 209 " pdb=" C SER C 209 " pdb=" N HIS C 210 " pdb=" CA HIS C 210 " ideal model delta harmonic sigma weight residual -180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CG ARG B 253 " pdb=" CD ARG B 253 " pdb=" NE ARG B 253 " pdb=" CZ ARG B 253 " ideal model delta sinusoidal sigma weight residual 90.00 41.43 48.57 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA ASP B 37 " pdb=" CB ASP B 37 " pdb=" CG ASP B 37 " pdb=" OD1 ASP B 37 " ideal model delta sinusoidal sigma weight residual -30.00 -88.05 58.05 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 6066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1355 0.069 - 0.137: 124 0.137 - 0.206: 3 0.206 - 0.275: 0 0.275 - 0.344: 1 Chirality restraints: 1483 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ILE B 83 " pdb=" N ILE B 83 " pdb=" C ILE B 83 " pdb=" CB ILE B 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CG LEU C 56 " pdb=" CB LEU C 56 " pdb=" CD1 LEU C 56 " pdb=" CD2 LEU C 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1480 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 122 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ASP C 122 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 122 " 0.016 2.00e-02 2.50e+03 pdb=" N SER C 123 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 403 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO C 404 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 403 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 404 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " -0.022 5.00e-02 4.00e+02 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1332 2.75 - 3.29: 9489 3.29 - 3.83: 16442 3.83 - 4.36: 18515 4.36 - 4.90: 32685 Nonbonded interactions: 78463 Sorted by model distance: nonbonded pdb=" OD1 ASP C 396 " pdb=" OG1 THR C 426 " model vdw 2.217 3.040 nonbonded pdb=" N GLU F 168 " pdb=" OE1 GLU F 168 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASN B 96 " pdb=" NE2 GLN C 362 " model vdw 2.276 3.120 nonbonded pdb=" OD1 ASP B 396 " pdb=" OG1 THR B 426 " model vdw 2.283 3.040 nonbonded pdb=" OG SER B 450 " pdb=" OE1 GLU B 452 " model vdw 2.290 3.040 ... (remaining 78458 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 'B' and (resid 1 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 500 or (resid 501 and (name N or \ name CA or name C or name O or name CB )) or resid 502 through 551)) selection = (chain 'C' and (resid 1 through 76 or (resid 77 and (name N or name CA or name C \ or name O or name CB )) or resid 78 through 256 or resid 310 through 444 or (re \ sid 445 and (name N or name CA or name C or name O or name CB )) or resid 446 th \ rough 551)) } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.160 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.003 0.155 10022 Z= 0.147 Angle : 0.802 52.143 13550 Z= 0.341 Chirality : 0.040 0.344 1483 Planarity : 0.004 0.049 1763 Dihedral : 17.855 89.515 3759 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.85 % Allowed : 28.95 % Favored : 69.20 % 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: 1.41 (0.24), residues: 1203 helix: 2.08 (0.23), residues: 531 sheet: 0.42 (0.39), residues: 186 loop : -0.08 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 7 TYR 0.020 0.001 TYR C 249 PHE 0.015 0.001 PHE C 365 TRP 0.007 0.001 TRP C 246 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (10018) covalent geometry : angle 0.61550 / 0.33 (13544) hydrogen bonds : bond 0.15020 / 10.14 ( 489) hydrogen bonds : angle 5.57676 / 3.87 ( 1377) metal coordination : bond 0.10316 / 4.94 ( 4) metal coordination : angle 24.47285 / 14.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 81 average time/residue: 0.5569 time to fit residues: 48.7817 Evaluate side-chains 79 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3567 r_free = 0.3567 target = 0.096705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067554 restraints weight = 21558.844| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.65 r_work: 0.2903 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10022 Z= 0.109 Angle : 0.574 17.384 13550 Z= 0.271 Chirality : 0.041 0.246 1483 Planarity : 0.004 0.051 1763 Dihedral : 5.957 60.878 1348 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.33 % Allowed : 25.44 % Favored : 71.23 % 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: 1.59 (0.24), residues: 1203 helix: 2.34 (0.22), residues: 535 sheet: 0.47 (0.39), residues: 187 loop : -0.15 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 7 TYR 0.024 0.001 TYR C 249 PHE 0.011 0.001 PHE B 454 TRP 0.007 0.001 TRP C 246 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10018) covalent geometry : angle 0.52732 / 0.27 (13544) hydrogen bonds : bond 0.04200 / 2.80 ( 489) hydrogen bonds : angle 4.45489 / 3.09 ( 1377) metal coordination : bond 0.00555 / 0.27 ( 4) metal coordination : angle 10.74180 / 5.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8679 (tp30) REVERT: B 81 LEU cc_start: 0.8392 (tp) cc_final: 0.8145 (mp) REVERT: B 219 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 251 HIS cc_start: 0.8935 (t-90) cc_final: 0.8647 (t70) REVERT: C 439 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8266 (ptt90) REVERT: F 20 ARG cc_start: 0.8932 (ptp-110) cc_final: 0.8562 (ppt170) outliers start: 36 outliers final: 10 residues processed: 94 average time/residue: 0.5855 time to fit residues: 59.3334 Evaluate side-chains 76 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 110 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3574 r_free = 0.3574 target = 0.097010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.067810 restraints weight = 21554.272| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.67 r_work: 0.2900 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10022 Z= 0.105 Angle : 0.535 13.234 13550 Z= 0.256 Chirality : 0.040 0.235 1483 Planarity : 0.003 0.050 1763 Dihedral : 5.325 61.271 1331 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.05 % Allowed : 25.16 % Favored : 71.79 % 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: 1.67 (0.24), residues: 1203 helix: 2.46 (0.22), residues: 534 sheet: 0.43 (0.38), residues: 189 loop : -0.14 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 253 TYR 0.013 0.001 TYR B 59 PHE 0.011 0.001 PHE F 16 TRP 0.006 0.001 TRP C 246 HIS 0.008 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10018) covalent geometry : angle 0.50653 / 0.25 (13544) hydrogen bonds : bond 0.03870 / 2.59 ( 489) hydrogen bonds : angle 4.24193 / 2.94 ( 1377) metal coordination : bond 0.00325 / 0.12 ( 4) metal coordination : angle 8.24076 / 4.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 19 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: B 62 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8691 (tp30) REVERT: B 81 LEU cc_start: 0.8472 (tp) cc_final: 0.8268 (mp) REVERT: B 219 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7866 (p) REVERT: C 251 HIS cc_start: 0.8932 (t-90) cc_final: 0.8464 (t70) REVERT: C 439 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8269 (ptt90) REVERT: F 20 ARG cc_start: 0.9106 (ptp-110) cc_final: 0.8642 (ppt170) outliers start: 33 outliers final: 10 residues processed: 96 average time/residue: 0.5263 time to fit residues: 54.5286 Evaluate side-chains 80 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN B 48 GLN B 197 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063229 restraints weight = 21932.513| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.63 r_work: 0.2784 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10022 Z= 0.262 Angle : 0.653 14.386 13550 Z= 0.317 Chirality : 0.045 0.224 1483 Planarity : 0.004 0.054 1763 Dihedral : 5.473 56.210 1329 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.52 % Allowed : 24.98 % Favored : 71.51 % 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: 1.33 (0.24), residues: 1203 helix: 2.07 (0.22), residues: 545 sheet: 0.38 (0.38), residues: 184 loop : -0.28 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 253 TYR 0.022 0.002 TYR C 249 PHE 0.014 0.002 PHE B 65 TRP 0.008 0.001 TRP C 44 HIS 0.004 0.001 HIS F 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.26 (10018) covalent geometry : angle 0.62034 / 0.31 (13544) hydrogen bonds : bond 0.05481 / 3.66 ( 489) hydrogen bonds : angle 4.47647 / 3.12 ( 1377) metal coordination : bond 0.00845 / 0.38 ( 4) metal coordination : angle 9.71656 / 4.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 19 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: B 62 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8772 (tp30) REVERT: B 68 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8302 (mmt-90) REVERT: B 81 LEU cc_start: 0.8594 (tp) cc_final: 0.8346 (mp) REVERT: B 219 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 452 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: C 187 TRP cc_start: 0.8728 (OUTLIER) cc_final: 0.7551 (m-10) REVERT: C 251 HIS cc_start: 0.8876 (t-90) cc_final: 0.8596 (t70) REVERT: C 253 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (ttm110) REVERT: C 439 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8377 (ptt90) REVERT: F 20 ARG cc_start: 0.9144 (ptp-110) cc_final: 0.8697 (ppt170) REVERT: F 52 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8569 (mtm110) outliers start: 38 outliers final: 15 residues processed: 96 average time/residue: 0.5365 time to fit residues: 55.3778 Evaluate side-chains 85 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 52 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067027 restraints weight = 21416.697| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.64 r_work: 0.2882 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10022 Z= 0.105 Angle : 0.545 10.484 13550 Z= 0.264 Chirality : 0.041 0.244 1483 Planarity : 0.003 0.052 1763 Dihedral : 5.206 58.359 1329 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.33 % Allowed : 25.72 % Favored : 70.95 % 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: 1.55 (0.24), residues: 1203 helix: 2.40 (0.22), residues: 535 sheet: 0.36 (0.39), residues: 185 loop : -0.24 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 253 TYR 0.012 0.001 TYR B 59 PHE 0.012 0.001 PHE F 16 TRP 0.008 0.001 TRP C 246 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10018) covalent geometry : angle 0.52681 / 0.26 (13544) hydrogen bonds : bond 0.03825 / 2.57 ( 489) hydrogen bonds : angle 4.14043 / 2.88 ( 1377) metal coordination : bond 0.00320 / 0.13 ( 4) metal coordination : angle 6.73094 / 3.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 19 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: B 62 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8692 (tp30) REVERT: B 68 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8204 (mmt-90) REVERT: B 81 LEU cc_start: 0.8527 (tp) cc_final: 0.8189 (mp) REVERT: B 219 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 253 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8063 (mtp85) REVERT: B 452 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: C 38 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: C 70 MET cc_start: 0.9264 (ttp) cc_final: 0.9050 (ttm) REVERT: C 187 TRP cc_start: 0.8665 (OUTLIER) cc_final: 0.7958 (m-10) REVERT: C 251 HIS cc_start: 0.8844 (t-90) cc_final: 0.8517 (t70) REVERT: C 351 GLN cc_start: 0.6787 (mp10) cc_final: 0.6513 (mp10) REVERT: C 439 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8280 (ptt90) outliers start: 36 outliers final: 13 residues processed: 103 average time/residue: 0.6110 time to fit residues: 67.3187 Evaluate side-chains 87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3553 r_free = 0.3553 target = 0.095817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066944 restraints weight = 21829.863| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.64 r_work: 0.2886 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10022 Z= 0.108 Angle : 0.551 10.266 13550 Z= 0.269 Chirality : 0.040 0.262 1483 Planarity : 0.004 0.051 1763 Dihedral : 5.118 59.012 1329 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.33 % Allowed : 26.36 % Favored : 70.31 % 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: 1.57 (0.24), residues: 1203 helix: 2.35 (0.22), residues: 543 sheet: 0.43 (0.38), residues: 186 loop : -0.23 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 127 TYR 0.023 0.001 TYR C 249 PHE 0.010 0.001 PHE B 444 TRP 0.008 0.001 TRP C 246 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10018) covalent geometry : angle 0.53522 / 0.27 (13544) hydrogen bonds : bond 0.03774 / 2.53 ( 489) hydrogen bonds : angle 4.05224 / 2.82 ( 1377) metal coordination : bond 0.00257 / 0.11 ( 4) metal coordination : angle 6.26402 / 3.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9159 (tpp80) cc_final: 0.8584 (mmm160) REVERT: B 19 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 62 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8705 (tp30) REVERT: B 68 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8201 (mmt-90) REVERT: B 81 LEU cc_start: 0.8475 (tp) cc_final: 0.8240 (mp) REVERT: B 219 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 253 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8050 (mtp85) REVERT: B 466 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: C 23 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7982 (pp30) REVERT: C 38 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: C 187 TRP cc_start: 0.8672 (OUTLIER) cc_final: 0.7954 (m-10) REVERT: C 251 HIS cc_start: 0.8843 (t-90) cc_final: 0.8514 (t70) REVERT: C 253 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8875 (ttm110) REVERT: C 351 GLN cc_start: 0.6776 (mp10) cc_final: 0.6490 (mp10) REVERT: C 365 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8585 (t80) REVERT: C 439 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8255 (ptt90) outliers start: 36 outliers final: 15 residues processed: 98 average time/residue: 0.6619 time to fit residues: 69.2483 Evaluate side-chains 91 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 0.0030 chunk 19 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3570 r_free = 0.3570 target = 0.096776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.067910 restraints weight = 21455.958| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.63 r_work: 0.2898 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10022 Z= 0.101 Angle : 0.549 10.607 13550 Z= 0.267 Chirality : 0.040 0.275 1483 Planarity : 0.004 0.050 1763 Dihedral : 5.081 59.984 1329 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 26.64 % Favored : 70.58 % 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: 1.57 (0.24), residues: 1203 helix: 2.39 (0.22), residues: 543 sheet: 0.35 (0.38), residues: 188 loop : -0.23 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 321 TYR 0.011 0.001 TYR C 105 PHE 0.011 0.001 PHE B 454 TRP 0.008 0.001 TRP C 246 HIS 0.003 0.000 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10018) covalent geometry : angle 0.53565 / 0.27 (13544) hydrogen bonds : bond 0.03522 / 2.36 ( 489) hydrogen bonds : angle 3.99418 / 2.78 ( 1377) metal coordination : bond 0.00196 / 0.09 ( 4) metal coordination : angle 5.66940 / 2.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8604 (mmm160) REVERT: B 19 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: B 62 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8705 (tp30) REVERT: B 68 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8234 (mmt-90) REVERT: B 81 LEU cc_start: 0.8613 (tp) cc_final: 0.8344 (mp) REVERT: B 390 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8055 (ptt90) REVERT: B 466 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: C 187 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.8016 (m-10) REVERT: C 251 HIS cc_start: 0.8832 (t-90) cc_final: 0.8480 (t70) REVERT: C 253 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8894 (ttm110) REVERT: C 351 GLN cc_start: 0.6791 (mp10) cc_final: 0.6519 (mp10) REVERT: C 365 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8562 (t80) REVERT: C 439 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8298 (ptt90) outliers start: 30 outliers final: 16 residues processed: 92 average time/residue: 0.6231 time to fit residues: 61.4181 Evaluate side-chains 89 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3556 r_free = 0.3556 target = 0.095956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.067021 restraints weight = 21406.596| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.61 r_work: 0.2883 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10022 Z= 0.121 Angle : 0.554 10.272 13550 Z= 0.269 Chirality : 0.041 0.264 1483 Planarity : 0.003 0.051 1763 Dihedral : 5.082 59.707 1329 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.24 % Allowed : 26.83 % Favored : 69.94 % 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: 1.63 (0.24), residues: 1203 helix: 2.48 (0.22), residues: 537 sheet: 0.39 (0.39), residues: 185 loop : -0.23 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 127 TYR 0.023 0.001 TYR C 249 PHE 0.010 0.001 PHE B 454 TRP 0.008 0.001 TRP C 246 HIS 0.009 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (10018) covalent geometry : angle 0.54021 / 0.27 (13544) hydrogen bonds : bond 0.03742 / 2.51 ( 489) hydrogen bonds : angle 4.01871 / 2.80 ( 1377) metal coordination : bond 0.00260 / 0.12 ( 4) metal coordination : angle 5.88567 / 3.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8594 (mmm160) REVERT: B 19 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: B 62 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8723 (tp30) REVERT: B 68 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8177 (mmt-90) REVERT: B 81 LEU cc_start: 0.8593 (tp) cc_final: 0.8311 (mp) REVERT: B 390 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8113 (ptt90) REVERT: B 466 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: C 172 ARG cc_start: 0.8162 (mpp-170) cc_final: 0.7802 (mmp-170) REVERT: C 187 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: C 251 HIS cc_start: 0.8844 (t-90) cc_final: 0.8479 (t70) REVERT: C 253 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8850 (ttm110) REVERT: C 351 GLN cc_start: 0.6849 (mp10) cc_final: 0.6587 (mp10) REVERT: C 365 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8589 (t80) REVERT: C 439 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8290 (ptt90) outliers start: 35 outliers final: 18 residues processed: 96 average time/residue: 0.6464 time to fit residues: 66.4695 Evaluate side-chains 90 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3560 r_free = 0.3560 target = 0.096152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067229 restraints weight = 21483.116| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.63 r_work: 0.2885 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10022 Z= 0.116 Angle : 0.563 10.412 13550 Z= 0.273 Chirality : 0.041 0.264 1483 Planarity : 0.004 0.051 1763 Dihedral : 5.075 59.787 1329 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.78 % Allowed : 27.47 % Favored : 69.75 % 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: 1.58 (0.24), residues: 1203 helix: 2.42 (0.22), residues: 542 sheet: 0.35 (0.39), residues: 186 loop : -0.25 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 253 TYR 0.011 0.001 TYR C 105 PHE 0.010 0.001 PHE C 72 TRP 0.008 0.001 TRP C 246 HIS 0.003 0.000 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10018) covalent geometry : angle 0.55035 / 0.27 (13544) hydrogen bonds : bond 0.03681 / 2.47 ( 489) hydrogen bonds : angle 4.00387 / 2.78 ( 1377) metal coordination : bond 0.00255 / 0.12 ( 4) metal coordination : angle 5.71415 / 2.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8605 (mmm160) REVERT: B 19 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 62 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8719 (tp30) REVERT: B 68 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8156 (mmt-90) REVERT: B 81 LEU cc_start: 0.8600 (tp) cc_final: 0.8293 (mp) REVERT: B 390 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8076 (ptt90) REVERT: B 466 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: C 172 ARG cc_start: 0.8217 (mpp-170) cc_final: 0.7867 (mmp-170) REVERT: C 187 TRP cc_start: 0.8687 (OUTLIER) cc_final: 0.8063 (m-10) REVERT: C 253 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8896 (ttm110) REVERT: C 351 GLN cc_start: 0.6864 (mp10) cc_final: 0.6605 (mp10) REVERT: C 365 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8601 (t80) REVERT: C 439 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8279 (ptt90) outliers start: 30 outliers final: 18 residues processed: 89 average time/residue: 0.6349 time to fit residues: 60.4154 Evaluate side-chains 91 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3564 r_free = 0.3564 target = 0.096383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067549 restraints weight = 21277.383| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.59 r_work: 0.2892 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10022 Z= 0.114 Angle : 0.569 10.185 13550 Z= 0.275 Chirality : 0.040 0.242 1483 Planarity : 0.004 0.051 1763 Dihedral : 5.079 60.028 1329 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.59 % Allowed : 27.29 % Favored : 70.12 % 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: 1.60 (0.24), residues: 1203 helix: 2.45 (0.22), residues: 542 sheet: 0.33 (0.38), residues: 186 loop : -0.24 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 253 TYR 0.026 0.001 TYR C 249 PHE 0.014 0.001 PHE B 454 TRP 0.008 0.001 TRP C 246 HIS 0.004 0.000 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (10018) covalent geometry : angle 0.55680 / 0.27 (13544) hydrogen bonds : bond 0.03617 / 2.42 ( 489) hydrogen bonds : angle 3.97958 / 2.77 ( 1377) metal coordination : bond 0.00238 / 0.11 ( 4) metal coordination : angle 5.64943 / 2.92 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9201 (tpp80) cc_final: 0.8607 (mmm160) REVERT: B 62 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8716 (tp30) REVERT: B 68 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8178 (mmt-90) REVERT: B 70 MET cc_start: 0.8943 (ttm) cc_final: 0.8709 (mmm) REVERT: B 81 LEU cc_start: 0.8549 (tp) cc_final: 0.8188 (mp) REVERT: B 390 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8040 (ptt90) REVERT: B 466 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: C 187 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: C 253 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8845 (ttm110) REVERT: C 351 GLN cc_start: 0.6863 (mp10) cc_final: 0.6589 (mp10) REVERT: C 365 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8601 (t80) REVERT: C 439 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8287 (ptt90) outliers start: 28 outliers final: 16 residues processed: 87 average time/residue: 0.6222 time to fit residues: 58.0243 Evaluate side-chains 87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain F residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 0.0070 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 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 = 0.3548 r_free = 0.3548 target = 0.095425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066247 restraints weight = 21551.187| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.65 r_work: 0.2865 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10022 Z= 0.146 Angle : 0.604 12.581 13550 Z= 0.292 Chirality : 0.041 0.296 1483 Planarity : 0.004 0.052 1763 Dihedral : 4.868 58.835 1326 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.41 % Allowed : 27.29 % Favored : 70.31 % 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: 1.57 (0.24), residues: 1203 helix: 2.42 (0.22), residues: 542 sheet: 0.33 (0.38), residues: 184 loop : -0.25 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 253 TYR 0.010 0.001 TYR C 105 PHE 0.011 0.001 PHE B 454 TRP 0.008 0.001 TRP C 246 HIS 0.005 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10018) covalent geometry : angle 0.58966 / 0.29 (13544) hydrogen bonds : bond 0.04019 / 2.69 ( 489) hydrogen bonds : angle 4.04709 / 2.81 ( 1377) metal coordination : bond 0.00375 / 0.17 ( 4) metal coordination : angle 6.20367 / 3.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3213.31 seconds wall clock time: 55 minutes 35.04 seconds (3335.04 seconds total)