Starting phenix.real_space_refine on Wed Aug 5 13:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22bv_68159/08_2026/22bv_68159.cif Found real_map, /net/cci-nas-00/data/ceres_data/22bv_68159/08_2026/22bv_68159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22bv_68159/08_2026/22bv_68159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22bv_68159/08_2026/22bv_68159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22bv_68159/08_2026/22bv_68159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22bv_68159/08_2026/22bv_68159.map" } resolution = 2.35 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 4 5.49 5 S 31 5.16 5 C 6194 2.51 5 N 1733 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 9839 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 4020 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: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4043 Classifications: {'peptide': 500} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 482} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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': 2} Link IDs: {'PTRANS': 10, 'TRANS': 204} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} 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 8413 SG CYS F 43 66.336 49.633 87.115 1.00123.74 S ATOM 8436 SG CYS F 46 65.876 52.445 84.988 1.00 95.08 S ATOM 8693 SG CYS F 78 63.123 48.995 85.001 1.00141.70 S ATOM 8777 SG CYS F 90 65.477 48.857 82.694 1.00154.04 S Time building chain proxies: 2.13, per 1000 atoms: 0.22 Number of scatterers: 9839 At special positions: 0 Unit cell: (108.48, 106.56, 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 4 15.00 O 1876 8.00 N 1733 7.00 C 6194 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: 0.92 Conformation dependent library (CDL) restraints added in 342.1 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 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " 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: 52 helices and 8 sheets defined 51.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 1 through 12 removed outlier: 3.816A pdb=" N LEU B 5 " --> pdb=" O VAL B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.562A pdb=" N ALA B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N HIS B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.551A pdb=" N GLN B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 120 removed outlier: 3.621A pdb=" N ILE B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.654A pdb=" N ARG B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.590A 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 removed outlier: 3.626A pdb=" N ARG B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 239 through 255 removed outlier: 3.531A pdb=" N PHE B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 Processing helix chain 'B' and resid 359 through 380 Processing helix chain 'B' and resid 385 through 389 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 550 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 13 through 28 removed outlier: 3.740A pdb=" N ALA C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 48 Processing helix chain 'C' and resid 99 through 120 removed outlier: 3.683A pdb=" N ILE C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TRP C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.757A pdb=" N ARG C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 403 through 418 removed outlier: 3.885A pdb=" N GLU C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 411 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 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 488 through 498 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: 3.806A pdb=" N HIS F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE F 16 " --> pdb=" O HIS F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 26 Processing helix chain 'F' and resid 27 through 40 removed outlier: 3.756A 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 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: 4.291A pdb=" N GLU F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLU F 169 " --> pdb=" O TYR F 165 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 198 removed outlier: 4.101A pdb=" N ASN F 198 " --> pdb=" O GLN F 194 " (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 50 through 51 removed outlier: 3.975A pdb=" N HIS B 60 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 165 removed outlier: 4.700A pdb=" N LYS B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N PHE B 151 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 10.954A pdb=" N PHE B 142 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE B 75 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 69 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 150 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 67 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU B 453 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN B 80 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU B 455 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP B 82 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 454 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 445 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 456 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG B 442 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 91 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE B 444 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE B 93 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N GLN B 446 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR B 90 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 200 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU B 394 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 202 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP B 396 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR B 204 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 330 through 336 removed outlier: 4.126A 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: 5.401A pdb=" N LEU C 67 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE C 150 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 69 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE C 75 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N PHE C 142 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 151 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 4.922A 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: 6.523A pdb=" N GLY C 391 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL C 424 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 393 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 426 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE C 395 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR C 90 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG C 442 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE C 91 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE C 444 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ILE C 93 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 9.982A 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: 4.310A 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 120 479 hydrogen bonds defined for protein. 1350 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: 1.59 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1675 1.31 - 1.44: 2661 1.44 - 1.57: 5649 1.57 - 1.69: 7 1.69 - 1.82: 51 Bond restraints: 10043 Sorted by residual: bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C GLY B 97 " pdb=" N GLN B 98 " ideal model delta sigma weight residual 1.334 1.406 -0.072 1.46e-02 4.69e+03 2.43e+01 bond pdb=" C5 ADP C 601 " pdb=" C6 ADP C 601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 ADP B 601 " pdb=" C6 ADP B 601 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 10038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 13424 2.82 - 5.65: 124 5.65 - 8.47: 22 8.47 - 11.29: 11 11.29 - 14.11: 2 Bond angle restraints: 13583 Sorted by residual: angle pdb=" CA GLY C 97 " pdb=" C GLY C 97 " pdb=" O GLY C 97 " ideal model delta sigma weight residual 119.19 126.42 -7.23 1.22e+00 6.72e-01 3.52e+01 angle pdb=" CA GLY B 97 " pdb=" C GLY B 97 " pdb=" N GLN B 98 " ideal model delta sigma weight residual 117.61 111.36 6.25 1.20e+00 6.94e-01 2.72e+01 angle pdb=" N ILE F 92 " pdb=" CA ILE F 92 " pdb=" C ILE F 92 " ideal model delta sigma weight residual 112.50 105.36 7.14 1.39e+00 5.18e-01 2.64e+01 angle pdb=" PA ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sigma weight residual 120.50 134.61 -14.11 3.00e+00 1.11e-01 2.21e+01 angle pdb=" CA GLY C 97 " pdb=" C GLY C 97 " pdb=" N GLN C 98 " ideal model delta sigma weight residual 118.39 113.28 5.11 1.18e+00 7.18e-01 1.88e+01 ... (remaining 13578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 5601 27.64 - 55.28: 423 55.28 - 82.92: 46 82.92 - 110.55: 8 110.55 - 138.19: 2 Dihedral angle restraints: 6080 sinusoidal: 2536 harmonic: 3544 Sorted by residual: dihedral pdb=" C5' ADP C 601 " pdb=" O5' ADP C 601 " pdb=" PA ADP C 601 " pdb=" O2A ADP C 601 " ideal model delta sinusoidal sigma weight residual 300.00 161.81 138.19 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 -175.88 115.88 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" CA HIS C 210 " pdb=" C HIS C 210 " pdb=" N PRO C 211 " pdb=" CA PRO C 211 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 6077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1043 0.035 - 0.069: 304 0.069 - 0.104: 98 0.104 - 0.138: 36 0.138 - 0.173: 6 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CA GLN B 357 " pdb=" N GLN B 357 " pdb=" C GLN B 357 " pdb=" CB GLN B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CB ILE F 196 " pdb=" CA ILE F 196 " pdb=" CG1 ILE F 196 " pdb=" CG2 ILE F 196 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 1484 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 97 " 0.035 2.00e-02 2.50e+03 7.16e-02 5.13e+01 pdb=" C GLY B 97 " -0.124 2.00e-02 2.50e+03 pdb=" O GLY B 97 " 0.049 2.00e-02 2.50e+03 pdb=" N GLN B 98 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 457 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO B 458 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 21 " 0.069 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO F 22 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " 0.054 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 992 2.75 - 3.29: 9978 3.29 - 3.82: 16527 3.82 - 4.36: 19019 4.36 - 4.90: 32727 Nonbonded interactions: 79243 Sorted by model distance: nonbonded pdb=" N GLU F 168 " pdb=" OE1 GLU F 168 " model vdw 2.209 3.120 nonbonded pdb=" OD1 ASP C 396 " pdb=" OG1 THR C 426 " model vdw 2.215 3.040 nonbonded pdb=" N GLU C 356 " pdb=" OE1 GLU C 356 " model vdw 2.242 3.120 nonbonded pdb=" OG SER B 205 " pdb=" OE1 GLU B 207 " model vdw 2.243 3.040 nonbonded pdb=" O PRO C 199 " pdb=" OH TYR C 230 " model vdw 2.248 3.040 ... (remaining 79238 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 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 601)) selection = (chain 'C' and (resid 1 through 229 or (resid 230 and (name N or name CA or name \ C or name O or name CB )) or resid 231 through 256 or resid 310 through 444 or \ (resid 445 and (name N or name CA or name C or name O or name CB )) or resid 446 \ through 601)) } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.980 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:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.598 10047 Z= 0.345 Angle : 0.973 56.025 13589 Z= 0.402 Chirality : 0.040 0.173 1487 Planarity : 0.006 0.105 1764 Dihedral : 18.465 138.193 3770 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.39 % Allowed : 34.01 % Favored : 64.60 % 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: 1.25 (0.24), residues: 1203 helix: 2.03 (0.23), residues: 528 sheet: 0.57 (0.39), residues: 172 loop : -0.35 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 510 TYR 0.015 0.001 TYR B 59 PHE 0.018 0.001 PHE F 16 TRP 0.048 0.002 TRP C 39 HIS 0.002 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (10043) covalent geometry : angle 0.75915 / 0.39 (13583) hydrogen bonds : bond 0.13409 / 8.69 ( 479) hydrogen bonds : angle 5.80331 / 4.20 ( 1350) metal coordination : bond 0.41412 / 17.77 ( 4) metal coordination : angle 29.01206 / 15.71 ( 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 100 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 466 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7493 (tm-30) REVERT: C 126 GLN cc_start: 0.8822 (tt0) cc_final: 0.8591 (mt0) REVERT: C 507 GLU cc_start: 0.7918 (tp30) cc_final: 0.7472 (pp20) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.5241 time to fit residues: 55.1340 Evaluate side-chains 88 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 444 PHE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 454 PHE Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain F residue 26 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068354 restraints weight = 20769.550| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.56 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: 0.8603 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10047 Z= 0.197 Angle : 0.802 42.340 13589 Z= 0.363 Chirality : 0.045 0.184 1487 Planarity : 0.005 0.072 1764 Dihedral : 7.467 127.826 1354 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.44 % Allowed : 26.99 % Favored : 68.58 % 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: 0.98 (0.23), residues: 1203 helix: 1.75 (0.22), residues: 542 sheet: 0.44 (0.39), residues: 174 loop : -0.49 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 208 TYR 0.019 0.002 TYR B 105 PHE 0.022 0.002 PHE C 40 TRP 0.018 0.002 TRP F 23 HIS 0.005 0.001 HIS F 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (10043) covalent geometry : angle 0.69685 / 0.36 (13583) hydrogen bonds : bond 0.05729 / 3.79 ( 479) hydrogen bonds : angle 4.65847 / 3.34 ( 1350) metal coordination : bond 0.03245 / 1.64 ( 4) metal coordination : angle 18.91721 / 10.91 ( 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 149 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 ILE cc_start: 0.8952 (pp) cc_final: 0.8655 (mt) REVERT: B 466 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 126 GLN cc_start: 0.9060 (mt0) cc_final: 0.8817 (mt0) REVERT: C 332 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7996 (ttt-90) REVERT: C 488 TYR cc_start: 0.8571 (m-80) cc_final: 0.8328 (m-80) REVERT: C 491 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8521 (p) REVERT: F 23 TRP cc_start: 0.7196 (t-100) cc_final: 0.6691 (t-100) REVERT: F 27 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8609 (tp30) REVERT: F 61 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (tpp80) outliers start: 48 outliers final: 15 residues processed: 141 average time/residue: 0.5407 time to fit residues: 82.0338 Evaluate side-chains 95 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN C 428 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067890 restraints weight = 20763.447| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.51 r_work: 0.2877 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10047 Z= 0.139 Angle : 0.670 33.136 13589 Z= 0.302 Chirality : 0.041 0.141 1487 Planarity : 0.004 0.060 1764 Dihedral : 6.192 74.280 1343 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.60 % Allowed : 27.26 % Favored : 69.13 % 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: 1.25 (0.24), residues: 1203 helix: 2.00 (0.22), residues: 539 sheet: 0.40 (0.38), residues: 184 loop : -0.30 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.016 0.001 TYR B 105 PHE 0.017 0.001 PHE C 40 TRP 0.013 0.001 TRP F 23 HIS 0.003 0.001 HIS F 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10043) covalent geometry : angle 0.58075 / 0.30 (13583) hydrogen bonds : bond 0.04441 / 2.95 ( 479) hydrogen bonds : angle 4.42051 / 3.18 ( 1350) metal coordination : bond 0.00868 / 0.37 ( 4) metal coordination : angle 15.88377 / 9.10 ( 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 131 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ASN cc_start: 0.2952 (OUTLIER) cc_final: 0.2596 (t0) REVERT: B 172 ARG cc_start: 0.7264 (ptm-80) cc_final: 0.7054 (ptm-80) REVERT: B 245 GLU cc_start: 0.8981 (tt0) cc_final: 0.8605 (tt0) REVERT: B 249 TYR cc_start: 0.9245 (t80) cc_final: 0.8992 (t80) REVERT: B 253 ARG cc_start: 0.9032 (tpp80) cc_final: 0.8570 (tpp80) REVERT: C 126 GLN cc_start: 0.9075 (mt0) cc_final: 0.8821 (mt0) REVERT: C 332 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8130 (ttt-90) REVERT: F 61 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8434 (tpp80) outliers start: 39 outliers final: 18 residues processed: 125 average time/residue: 0.5262 time to fit residues: 71.1100 Evaluate side-chains 104 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ASN 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 394 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN C 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064871 restraints weight = 20964.798| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.52 r_work: 0.2811 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10047 Z= 0.151 Angle : 0.663 31.580 13589 Z= 0.305 Chirality : 0.041 0.144 1487 Planarity : 0.004 0.055 1764 Dihedral : 5.666 64.851 1339 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.70 % Allowed : 26.71 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1203 helix: 2.01 (0.22), residues: 537 sheet: 0.33 (0.38), residues: 186 loop : -0.35 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 17 TYR 0.017 0.001 TYR B 105 PHE 0.016 0.001 PHE B 243 TRP 0.013 0.001 TRP F 23 HIS 0.003 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (10043) covalent geometry : angle 0.59045 / 0.30 (13583) hydrogen bonds : bond 0.04699 / 3.11 ( 479) hydrogen bonds : angle 4.37428 / 3.14 ( 1350) metal coordination : bond 0.01401 / 0.62 ( 4) metal coordination : angle 14.37005 / 8.26 ( 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 130 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8832 (ptp-170) cc_final: 0.8523 (ptt-90) REVERT: B 24 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7282 (tm-30) REVERT: B 245 GLU cc_start: 0.9083 (tt0) cc_final: 0.8752 (tt0) REVERT: B 253 ARG cc_start: 0.9056 (tpp80) cc_final: 0.8517 (mmm-85) REVERT: C 126 GLN cc_start: 0.9093 (mt0) cc_final: 0.8810 (mt0) REVERT: C 172 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8268 (mpp-170) REVERT: F 27 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8645 (tp30) outliers start: 40 outliers final: 19 residues processed: 123 average time/residue: 0.5719 time to fit residues: 75.6993 Evaluate side-chains 97 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065247 restraints weight = 20786.680| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.50 r_work: 0.2834 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10047 Z= 0.127 Angle : 0.626 26.926 13589 Z= 0.290 Chirality : 0.040 0.145 1487 Planarity : 0.004 0.055 1764 Dihedral : 5.501 65.560 1339 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.33 % Allowed : 25.97 % Favored : 70.70 % 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: 1.31 (0.24), residues: 1203 helix: 2.11 (0.22), residues: 535 sheet: 0.39 (0.38), residues: 185 loop : -0.32 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 17 TYR 0.021 0.001 TYR B 249 PHE 0.014 0.001 PHE B 243 TRP 0.011 0.001 TRP F 23 HIS 0.002 0.001 HIS F 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10043) covalent geometry : angle 0.56661 / 0.29 (13583) hydrogen bonds : bond 0.04137 / 2.76 ( 479) hydrogen bonds : angle 4.26635 / 3.06 ( 1350) metal coordination : bond 0.01109 / 0.46 ( 4) metal coordination : angle 12.68248 / 7.26 ( 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 120 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8843 (ptp-170) cc_final: 0.8539 (ptt-90) REVERT: B 195 MET cc_start: 0.8794 (ttp) cc_final: 0.8457 (ttm) REVERT: B 245 GLU cc_start: 0.9093 (tt0) cc_final: 0.8763 (tt0) REVERT: B 253 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8542 (mmm-85) REVERT: C 126 GLN cc_start: 0.9118 (mt0) cc_final: 0.8832 (mt0) REVERT: C 249 TYR cc_start: 0.9210 (t80) cc_final: 0.8101 (t80) REVERT: C 253 ARG cc_start: 0.9104 (ttm-80) cc_final: 0.8514 (ttm110) REVERT: C 332 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: F 16 PHE cc_start: 0.7951 (m-10) cc_final: 0.7706 (m-10) outliers start: 36 outliers final: 20 residues processed: 113 average time/residue: 0.6234 time to fit residues: 75.3809 Evaluate side-chains 97 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 379 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.062917 restraints weight = 20918.995| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.50 r_work: 0.2770 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10047 Z= 0.147 Angle : 0.667 32.737 13589 Z= 0.306 Chirality : 0.041 0.145 1487 Planarity : 0.004 0.055 1764 Dihedral : 5.630 64.065 1339 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.87 % Allowed : 25.60 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1203 helix: 2.03 (0.22), residues: 537 sheet: 0.36 (0.38), residues: 186 loop : -0.37 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 172 TYR 0.016 0.001 TYR B 105 PHE 0.015 0.001 PHE B 243 TRP 0.015 0.001 TRP F 23 HIS 0.002 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10043) covalent geometry : angle 0.59178 / 0.30 (13583) hydrogen bonds : bond 0.04567 / 3.05 ( 479) hydrogen bonds : angle 4.27794 / 3.05 ( 1350) metal coordination : bond 0.01078 / 0.47 ( 4) metal coordination : angle 14.62165 / 8.40 ( 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 112 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.8897 (ptp-170) cc_final: 0.8540 (ptt-90) REVERT: B 245 GLU cc_start: 0.9081 (tt0) cc_final: 0.8691 (tt0) REVERT: B 253 ARG cc_start: 0.9133 (tpp80) cc_final: 0.8685 (mmm-85) REVERT: C 20 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8729 (mt) REVERT: C 126 GLN cc_start: 0.9155 (mt0) cc_final: 0.8854 (mt0) REVERT: C 332 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8154 (ttt-90) outliers start: 31 outliers final: 20 residues processed: 107 average time/residue: 0.5878 time to fit residues: 67.6815 Evaluate side-chains 96 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER 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 359 SER Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 23 GLN ** 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 = 0.3536 r_free = 0.3536 target = 0.093176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.065542 restraints weight = 20724.289| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.46 r_work: 0.2842 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10047 Z= 0.112 Angle : 0.632 27.727 13589 Z= 0.292 Chirality : 0.039 0.144 1487 Planarity : 0.004 0.056 1764 Dihedral : 5.468 66.159 1338 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.87 % Allowed : 25.51 % Favored : 71.63 % 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: 1.34 (0.24), residues: 1203 helix: 2.10 (0.22), residues: 542 sheet: 0.53 (0.38), residues: 184 loop : -0.35 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 172 TYR 0.022 0.001 TYR B 249 PHE 0.013 0.001 PHE B 243 TRP 0.008 0.001 TRP F 23 HIS 0.002 0.001 HIS B 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10043) covalent geometry : angle 0.57394 / 0.29 (13583) hydrogen bonds : bond 0.03781 / 2.53 ( 479) hydrogen bonds : angle 4.13081 / 2.94 ( 1350) metal coordination : bond 0.00894 / 0.42 ( 4) metal coordination : angle 12.63620 / 7.19 ( 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 113 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASN cc_start: 0.2565 (OUTLIER) cc_final: 0.2319 (t0) REVERT: B 245 GLU cc_start: 0.9109 (tt0) cc_final: 0.8851 (tt0) REVERT: B 253 ARG cc_start: 0.9089 (tpp80) cc_final: 0.8644 (mmm-85) REVERT: C 126 GLN cc_start: 0.9179 (mt0) cc_final: 0.8880 (mt0) REVERT: C 249 TYR cc_start: 0.9172 (t80) cc_final: 0.7993 (t80) REVERT: C 253 ARG cc_start: 0.9126 (ttm-80) cc_final: 0.8551 (ttm110) REVERT: C 255 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: C 446 GLN cc_start: 0.7417 (pm20) cc_final: 0.6487 (tp40) outliers start: 31 outliers final: 18 residues processed: 108 average time/residue: 0.5587 time to fit residues: 65.1798 Evaluate side-chains 96 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 102 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 394 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062525 restraints weight = 20926.476| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.49 r_work: 0.2761 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10047 Z= 0.145 Angle : 0.666 30.218 13589 Z= 0.310 Chirality : 0.040 0.144 1487 Planarity : 0.005 0.062 1764 Dihedral : 5.571 65.145 1336 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.50 % Allowed : 25.69 % Favored : 71.81 % 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: 1.27 (0.24), residues: 1203 helix: 2.03 (0.22), residues: 543 sheet: 0.51 (0.38), residues: 182 loop : -0.39 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 332 TYR 0.016 0.001 TYR B 105 PHE 0.014 0.001 PHE B 243 TRP 0.017 0.001 TRP F 23 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (10043) covalent geometry : angle 0.60361 / 0.31 (13583) hydrogen bonds : bond 0.04457 / 2.99 ( 479) hydrogen bonds : angle 4.24484 / 3.04 ( 1350) metal coordination : bond 0.01530 / 0.73 ( 4) metal coordination : angle 13.35474 / 7.63 ( 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 107 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8983 (mmmm) REVERT: B 41 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8561 (mm-30) REVERT: B 245 GLU cc_start: 0.9078 (tt0) cc_final: 0.8749 (tt0) REVERT: B 253 ARG cc_start: 0.9124 (tpp80) cc_final: 0.8719 (mmm-85) REVERT: C 126 GLN cc_start: 0.9167 (mt0) cc_final: 0.8865 (mt0) REVERT: C 253 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8521 (ttm110) REVERT: C 446 GLN cc_start: 0.7630 (pm20) cc_final: 0.6776 (tp40) outliers start: 27 outliers final: 16 residues processed: 102 average time/residue: 0.6085 time to fit residues: 66.7507 Evaluate side-chains 90 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER 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 379 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN B 48 GLN B 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060594 restraints weight = 20862.301| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.49 r_work: 0.2722 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10047 Z= 0.180 Angle : 0.708 34.138 13589 Z= 0.327 Chirality : 0.042 0.165 1487 Planarity : 0.005 0.060 1764 Dihedral : 5.835 62.909 1336 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.40 % Allowed : 25.79 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1203 helix: 1.89 (0.22), residues: 544 sheet: 0.39 (0.38), residues: 183 loop : -0.46 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 332 TYR 0.024 0.002 TYR B 249 PHE 0.013 0.001 PHE B 243 TRP 0.014 0.001 TRP F 23 HIS 0.003 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (10043) covalent geometry : angle 0.63416 / 0.32 (13583) hydrogen bonds : bond 0.04950 / 3.31 ( 479) hydrogen bonds : angle 4.37009 / 3.13 ( 1350) metal coordination : bond 0.01503 / 0.72 ( 4) metal coordination : angle 15.02060 / 8.69 ( 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 102 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9051 (ttp-110) cc_final: 0.8793 (ttp-110) REVERT: B 28 ASN cc_start: 0.2391 (OUTLIER) cc_final: 0.2104 (t0) REVERT: B 245 GLU cc_start: 0.9052 (tt0) cc_final: 0.8697 (tt0) REVERT: B 253 ARG cc_start: 0.9130 (tpp80) cc_final: 0.8729 (mmm-85) REVERT: C 126 GLN cc_start: 0.9174 (mt0) cc_final: 0.8857 (mt0) REVERT: C 253 ARG cc_start: 0.9135 (ttm-80) cc_final: 0.8580 (ttm110) REVERT: C 446 GLN cc_start: 0.7998 (pm20) cc_final: 0.7151 (tp40) outliers start: 26 outliers final: 16 residues processed: 95 average time/residue: 0.6567 time to fit residues: 66.7887 Evaluate side-chains 92 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN ** C 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064067 restraints weight = 20490.701| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.42 r_work: 0.2813 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10047 Z= 0.124 Angle : 0.670 27.107 13589 Z= 0.316 Chirality : 0.040 0.172 1487 Planarity : 0.005 0.068 1764 Dihedral : 5.607 65.117 1336 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.66 % Allowed : 26.06 % Favored : 72.27 % 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: 1.23 (0.24), residues: 1203 helix: 2.03 (0.22), residues: 544 sheet: 0.43 (0.38), residues: 183 loop : -0.43 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 17 TYR 0.023 0.001 TYR B 249 PHE 0.014 0.001 PHE F 16 TRP 0.009 0.001 TRP C 334 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (10043) covalent geometry : angle 0.62103 / 0.31 (13583) hydrogen bonds : bond 0.04001 / 2.69 ( 479) hydrogen bonds : angle 4.22936 / 3.04 ( 1350) metal coordination : bond 0.01191 / 0.56 ( 4) metal coordination : angle 12.02824 / 6.86 ( 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 95 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8794 (ttp-110) REVERT: B 28 ASN cc_start: 0.2012 (OUTLIER) cc_final: 0.1630 (t0) REVERT: B 245 GLU cc_start: 0.9090 (tt0) cc_final: 0.8826 (tt0) REVERT: B 253 ARG cc_start: 0.9098 (tpp80) cc_final: 0.8715 (mmm-85) REVERT: B 466 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: C 126 GLN cc_start: 0.9181 (mt0) cc_final: 0.8879 (mt0) REVERT: C 249 TYR cc_start: 0.9160 (t80) cc_final: 0.8024 (t80) REVERT: C 253 ARG cc_start: 0.9183 (ttm-80) cc_final: 0.8656 (ttm110) REVERT: C 446 GLN cc_start: 0.8057 (pm20) cc_final: 0.7327 (tp40) REVERT: F 16 PHE cc_start: 0.8166 (m-80) cc_final: 0.7907 (t80) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.7160 time to fit residues: 68.6622 Evaluate side-chains 92 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 0.0000 chunk 72 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 28 ASN C 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.065000 restraints weight = 20636.181| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.44 r_work: 0.2837 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10047 Z= 0.121 Angle : 0.669 24.324 13589 Z= 0.319 Chirality : 0.040 0.146 1487 Planarity : 0.005 0.067 1764 Dihedral : 5.484 66.527 1336 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.03 % Allowed : 26.16 % Favored : 71.81 % 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: 2.13 (0.22), residues: 543 sheet: 0.50 (0.38), residues: 183 loop : -0.40 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 17 TYR 0.022 0.001 TYR B 249 PHE 0.016 0.001 PHE B 85 TRP 0.008 0.001 TRP C 334 HIS 0.002 0.001 HIS B 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (10043) covalent geometry : angle 0.62893 / 0.32 (13583) hydrogen bonds : bond 0.03724 / 2.51 ( 479) hydrogen bonds : angle 4.18037 / 3.01 ( 1350) metal coordination : bond 0.01093 / 0.51 ( 4) metal coordination : angle 10.83798 / 6.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.76 seconds wall clock time: 66 minutes 57.07 seconds (4017.07 seconds total)