Starting phenix.real_space_refine on Fri Sep 11 00:40:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.map" model { file = "/net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u1n_20612/09_2026/6u1n_20612.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 102 atoms to isotropic. 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 P 6 5.49 5 S 15 5.16 5 Cl 1 4.86 5 C 3739 2.51 5 N 1012 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5863 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1660 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 10, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 767 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'PHE:plan': 13, 'GLU:plan': 5, 'ASN:plan1': 12, 'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 7, 'ASP:plan': 5, 'TRP:plan': 3, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 264 Chain: "C" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2547 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 331} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'GLU:plan': 20, 'ARG:plan': 9, 'GLN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 204 Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 846 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 52 Chain: "L" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 781 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.25 Number of scatterers: 5863 At special positions: 0 Unit cell: (118.72, 116.6, 90.1, 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) Cl 1 17.00 S 15 16.00 P 6 15.00 O 1090 8.00 N 1012 7.00 C 3739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 176 " distance=2.04 Simple disulfide: pdb=" SG CYS R 413 " - pdb=" SG CYS R 416 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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: 0.60 Conformation dependent library (CDL) restraints added in 434.6 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 11 sheets defined 32.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 20 through 48 removed outlier: 4.113A pdb=" N LEU R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY R 31 " --> pdb=" O VAL R 27 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL R 36 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 4.555A pdb=" N LEU R 62 " --> pdb=" O ASN R 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE R 71 " --> pdb=" O CYS R 67 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY R 73 " --> pdb=" O ASP R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 removed outlier: 3.859A pdb=" N THR R 81 " --> pdb=" O MET R 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 82 " --> pdb=" O ASN R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 117 removed outlier: 4.083A pdb=" N LEU R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA R 101 " --> pdb=" O ASP R 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 116 " --> pdb=" O MET R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 127 removed outlier: 3.766A pdb=" N VAL R 125 " --> pdb=" O ARG R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 167 removed outlier: 4.142A pdb=" N MET R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA R 147 " --> pdb=" O MET R 143 " (cutoff:3.500A) Proline residue: R 157 - end of helix removed outlier: 4.501A pdb=" N GLN R 163 " --> pdb=" O ILE R 159 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 213 removed outlier: 3.533A pdb=" N THR R 187 " --> pdb=" O ASN R 183 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY R 189 " --> pdb=" O ALA R 185 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA R 191 " --> pdb=" O THR R 187 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU R 197 " --> pdb=" O ALA R 193 " (cutoff:3.500A) Proline residue: R 198 - end of helix removed outlier: 3.756A pdb=" N ALA R 212 " --> pdb=" O HIS R 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 414 removed outlier: 4.234A pdb=" N LEU R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA R 391 " --> pdb=" O ARG R 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP R 400 " --> pdb=" O PHE R 396 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 401 " --> pdb=" O ILE R 397 " (cutoff:3.500A) Proline residue: R 402 - end of helix removed outlier: 4.086A pdb=" N LEU R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE R 409 " --> pdb=" O VAL R 405 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR R 411 " --> pdb=" O VAL R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 417 No H-bonds generated for 'chain 'R' and resid 415 through 417' Processing helix chain 'R' and resid 418 through 431 removed outlier: 3.734A pdb=" N THR R 423 " --> pdb=" O ASN R 419 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE R 424 " --> pdb=" O THR R 420 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR R 426 " --> pdb=" O TRP R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 441 Proline residue: R 437 - end of helix removed outlier: 3.747A pdb=" N TYR R 440 " --> pdb=" O ASN R 436 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA R 441 " --> pdb=" O PRO R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 444 through 452 Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.927A pdb=" N ARG C 282 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'H' and resid 56 through 59 Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.593A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.692A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'R' and resid 492 through 495 Processing sheet with id=AA2, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 87 removed outlier: 6.763A pdb=" N VAL C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 209 removed outlier: 4.065A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 318 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA C 239 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 320 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN C 237 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS C 322 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 235 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS C 324 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 233 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS C 326 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE C 231 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL C 328 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 227 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 241 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN C 248 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 10 Processing sheet with id=AA8, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.784A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.816A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.497A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 774 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: 0.90 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1004 1.32 - 1.46: 2108 1.46 - 1.59: 2846 1.59 - 1.73: 19 1.73 - 1.86: 21 Bond restraints: 5998 Sorted by residual: bond pdb=" C22 2CU R 601 " pdb=" S21 2CU R 601 " ideal model delta sigma weight residual 1.721 1.862 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C03 2CU R 601 " pdb=" N02 2CU R 601 " ideal model delta sigma weight residual 1.449 1.316 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C07 2CU R 601 " pdb=" N02 2CU R 601 " ideal model delta sigma weight residual 1.448 1.318 0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C08 2CU R 601 " pdb=" N05 2CU R 601 " ideal model delta sigma weight residual 1.346 1.476 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C01 2CU R 601 " pdb=" N02 2CU R 601 " ideal model delta sigma weight residual 1.445 1.323 0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 5993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 8151 2.64 - 5.28: 96 5.28 - 7.92: 14 7.92 - 10.55: 2 10.55 - 13.19: 3 Bond angle restraints: 8266 Sorted by residual: angle pdb=" OG1 TPO R 490 " pdb=" P TPO R 490 " pdb=" O1P TPO R 490 " ideal model delta sigma weight residual 100.43 113.62 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB TPO R 491 " pdb=" OG1 TPO R 491 " pdb=" P TPO R 491 " ideal model delta sigma weight residual 119.31 106.42 12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CB SEP R 493 " pdb=" OG SEP R 493 " pdb=" P SEP R 493 " ideal model delta sigma weight residual 110.00 120.57 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C17 2CU R 601 " pdb=" C18 2CU R 601 " pdb=" C20 2CU R 601 " ideal model delta sigma weight residual 111.70 122.11 -10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA HIS C 362 " pdb=" C HIS C 362 " pdb=" O HIS C 362 " ideal model delta sigma weight residual 122.14 118.31 3.83 1.24e+00 6.50e-01 9.53e+00 ... (remaining 8261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.11: 3441 29.11 - 58.21: 58 58.21 - 87.32: 5 87.32 - 116.42: 0 116.42 - 145.53: 1 Dihedral angle restraints: 3505 sinusoidal: 977 harmonic: 2528 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -154.52 68.52 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS R 413 " pdb=" SG CYS R 413 " pdb=" SG CYS R 416 " pdb=" CB CYS R 416 " ideal model delta sinusoidal sigma weight residual 93.00 150.39 -57.39 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" C29 2CU R 601 " pdb=" C27 2CU R 601 " pdb=" C28 2CU R 601 " pdb=" N26 2CU R 601 " ideal model delta sinusoidal sigma weight residual 250.71 105.18 145.53 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 3502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 806 0.055 - 0.111: 167 0.111 - 0.166: 16 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 991 Sorted by residual: chirality pdb=" C27 2CU R 601 " pdb=" C28 2CU R 601 " pdb=" C29 2CU R 601 " pdb=" N26 2CU R 601 " both_signs ideal model delta sigma weight residual True 2.31 2.59 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR L 92 " pdb=" N TYR L 92 " pdb=" C TYR L 92 " pdb=" CB TYR L 92 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 988 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 106 " 0.018 2.00e-02 2.50e+03 1.55e-02 6.02e+00 pdb=" CG TRP H 106 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP H 106 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 106 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 106 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 106 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 106 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 106 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 106 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 197 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO R 198 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO R 198 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 198 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER L 66 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C SER L 66 " -0.023 2.00e-02 2.50e+03 pdb=" O SER L 66 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG L 67 " 0.008 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 697 2.74 - 3.28: 6435 3.28 - 3.82: 9358 3.82 - 4.36: 10725 4.36 - 4.90: 17854 Nonbonded interactions: 45069 Sorted by model distance: nonbonded pdb=" O LYS C 195 " pdb=" OG1 THR C 224 " model vdw 2.198 3.040 nonbonded pdb=" NH1 ARG L 19 " pdb=" OG1 THR L 75 " model vdw 2.204 3.120 nonbonded pdb=" O ASN C 222 " pdb=" N SER C 265 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR H 63 " pdb=" N ILE H 73 " model vdw 2.248 3.120 nonbonded pdb=" OG1 THR C 183 " pdb=" O ALA C 201 " model vdw 2.255 3.040 ... (remaining 45064 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.008 0.141 6002 Z= 0.428 Angle : 0.809 13.192 8274 Z= 0.429 Chirality : 0.044 0.276 991 Planarity : 0.004 0.042 1056 Dihedral : 12.091 145.527 1861 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -4.67 (0.23), residues: 843 helix: -3.58 (0.23), residues: 186 sheet: -2.48 (0.29), residues: 263 loop : -3.24 (0.26), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 19 TYR 0.012 0.001 TYR L 50 PHE 0.020 0.002 PHE H 105 TRP 0.040 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.43 ( 5998) covalent geometry : angle 0.80788 / 0.43 ( 8266) SS BOND : bond 0.00558 / 0.27 ( 4) SS BOND : angle 1.61482 / 0.88 ( 8) hydrogen bonds : bond 0.23020 / 17.39 ( 284) hydrogen bonds : angle 9.34898 / 6.94 ( 774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.9037 (m-80) cc_final: 0.8462 (m-80) REVERT: C 257 GLU cc_start: 0.9068 (pt0) cc_final: 0.8855 (tm-30) REVERT: H 16 GLN cc_start: 0.8429 (mm110) cc_final: 0.8126 (mm-40) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0750 time to fit residues: 8.2381 Evaluate side-chains 61 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 58 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 172 GLN C 198 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.063604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045090 restraints weight = 32687.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046444 restraints weight = 17843.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047066 restraints weight = 12310.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047717 restraints weight = 10134.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047878 restraints weight = 8717.868| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6002 Z= 0.223 Angle : 0.613 8.113 8274 Z= 0.318 Chirality : 0.044 0.183 991 Planarity : 0.004 0.034 1056 Dihedral : 8.468 140.950 941 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.04 % Allowed : 15.22 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.26), residues: 843 helix: -1.62 (0.31), residues: 217 sheet: -1.93 (0.29), residues: 263 loop : -2.53 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 76 TYR 0.014 0.001 TYR R 131 PHE 0.016 0.002 PHE H 105 TRP 0.018 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 ( 5998) covalent geometry : angle 0.61163 / 0.32 ( 8266) SS BOND : bond 0.00504 / 0.25 ( 4) SS BOND : angle 1.24194 / 0.65 ( 8) hydrogen bonds : bond 0.04212 / 3.16 ( 284) hydrogen bonds : angle 6.43191 / 4.81 ( 774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8881 (m-80) cc_final: 0.8285 (m-80) REVERT: C 256 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8141 (tm-30) REVERT: H 16 GLN cc_start: 0.8334 (mm110) cc_final: 0.8085 (mm-40) REVERT: L 22 ILE cc_start: 0.9444 (mm) cc_final: 0.9229 (mt) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.0594 time to fit residues: 6.8606 Evaluate side-chains 69 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 0.0270 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 130 GLN C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.065857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047126 restraints weight = 31398.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048579 restraints weight = 16594.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049522 restraints weight = 11231.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050078 restraints weight = 8827.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050393 restraints weight = 7651.382| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6002 Z= 0.116 Angle : 0.565 8.077 8274 Z= 0.283 Chirality : 0.043 0.167 991 Planarity : 0.003 0.028 1056 Dihedral : 8.030 140.521 941 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.83 % Allowed : 15.87 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.04 (0.28), residues: 843 helix: -0.48 (0.35), residues: 224 sheet: -1.41 (0.31), residues: 261 loop : -1.75 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 76 TYR 0.007 0.001 TYR R 403 PHE 0.012 0.001 PHE R 396 TRP 0.013 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 5998) covalent geometry : angle 0.56436 / 0.28 ( 8266) SS BOND : bond 0.00354 / 0.18 ( 4) SS BOND : angle 1.19466 / 0.67 ( 8) hydrogen bonds : bond 0.03386 / 2.54 ( 284) hydrogen bonds : angle 5.67133 / 4.21 ( 774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8770 (m-10) cc_final: 0.8205 (m-80) REVERT: R 400 TRP cc_start: 0.7447 (m100) cc_final: 0.7064 (m100) REVERT: H 16 GLN cc_start: 0.8445 (mm110) cc_final: 0.8094 (mm-40) REVERT: L 22 ILE cc_start: 0.9408 (mm) cc_final: 0.9205 (mt) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 0.0659 time to fit residues: 7.6824 Evaluate side-chains 71 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 0.0470 chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 chunk 7 optimal weight: 20.0000 overall best weight: 2.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 16 GLN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045936 restraints weight = 31908.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.047284 restraints weight = 17110.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048173 restraints weight = 11760.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048724 restraints weight = 9301.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049083 restraints weight = 8052.381| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6002 Z= 0.174 Angle : 0.593 8.469 8274 Z= 0.296 Chirality : 0.043 0.161 991 Planarity : 0.003 0.029 1056 Dihedral : 8.019 140.693 941 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.57 % Allowed : 16.74 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.29), residues: 843 helix: 0.12 (0.36), residues: 216 sheet: -1.16 (0.32), residues: 257 loop : -1.59 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 121 TYR 0.010 0.001 TYR R 403 PHE 0.022 0.002 PHE H 30 TRP 0.014 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 5998) covalent geometry : angle 0.58905 / 0.29 ( 8266) SS BOND : bond 0.00469 / 0.23 ( 4) SS BOND : angle 2.39581 / 1.45 ( 8) hydrogen bonds : bond 0.03308 / 2.46 ( 284) hydrogen bonds : angle 5.59798 / 4.14 ( 774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8789 (m-10) cc_final: 0.8192 (m-80) REVERT: R 400 TRP cc_start: 0.7366 (m100) cc_final: 0.7038 (m100) REVERT: C 256 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7903 (tm-30) REVERT: H 16 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8011 (mm-40) REVERT: L 107 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8079 (tp) outliers start: 21 outliers final: 13 residues processed: 86 average time/residue: 0.0562 time to fit residues: 6.9855 Evaluate side-chains 76 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.066071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047344 restraints weight = 32104.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048770 restraints weight = 16805.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049690 restraints weight = 11391.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.050092 restraints weight = 8956.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050544 restraints weight = 7942.998| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6002 Z= 0.112 Angle : 0.571 7.977 8274 Z= 0.277 Chirality : 0.043 0.155 991 Planarity : 0.003 0.030 1056 Dihedral : 7.856 140.540 941 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.04 % Allowed : 19.35 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.10 (0.29), residues: 843 helix: 0.45 (0.36), residues: 222 sheet: -0.92 (0.32), residues: 255 loop : -1.22 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 7 TYR 0.007 0.001 TYR H 107 PHE 0.013 0.001 PHE H 105 TRP 0.013 0.001 TRP R 155 HIS 0.002 0.001 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 5998) covalent geometry : angle 0.56746 / 0.28 ( 8266) SS BOND : bond 0.00198 / 0.09 ( 4) SS BOND : angle 1.98845 / 1.21 ( 8) hydrogen bonds : bond 0.02971 / 2.22 ( 284) hydrogen bonds : angle 5.21392 / 3.85 ( 774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8750 (m-10) cc_final: 0.8181 (m-80) REVERT: R 400 TRP cc_start: 0.7400 (m100) cc_final: 0.7158 (m100) REVERT: H 16 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8203 (mm-40) REVERT: L 5 MET cc_start: 0.8606 (tpp) cc_final: 0.8333 (tpp) REVERT: L 99 PHE cc_start: 0.8999 (m-80) cc_final: 0.8753 (m-80) outliers start: 14 outliers final: 9 residues processed: 82 average time/residue: 0.0577 time to fit residues: 6.8158 Evaluate side-chains 73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.066737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047882 restraints weight = 32161.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049329 restraints weight = 16980.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050249 restraints weight = 11543.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050687 restraints weight = 9103.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051157 restraints weight = 8027.578| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6002 Z= 0.104 Angle : 0.561 9.501 8274 Z= 0.272 Chirality : 0.042 0.145 991 Planarity : 0.003 0.034 1056 Dihedral : 7.701 140.606 941 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.48 % Allowed : 20.43 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.30), residues: 843 helix: 0.95 (0.36), residues: 221 sheet: -0.81 (0.32), residues: 258 loop : -1.11 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 7 TYR 0.007 0.001 TYR H 107 PHE 0.011 0.001 PHE H 105 TRP 0.011 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 5998) covalent geometry : angle 0.56099 / 0.27 ( 8266) SS BOND : bond 0.00280 / 0.13 ( 4) SS BOND : angle 0.90012 / 0.51 ( 8) hydrogen bonds : bond 0.02871 / 2.13 ( 284) hydrogen bonds : angle 4.99975 / 3.69 ( 774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 TYR cc_start: 0.8679 (m-80) cc_final: 0.8466 (m-80) REVERT: R 119 PHE cc_start: 0.8751 (m-10) cc_final: 0.8162 (m-80) REVERT: L 107 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8165 (tp) outliers start: 16 outliers final: 12 residues processed: 77 average time/residue: 0.0628 time to fit residues: 6.9105 Evaluate side-chains 77 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.065153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046193 restraints weight = 32022.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047676 restraints weight = 17503.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048562 restraints weight = 11783.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049149 restraints weight = 9278.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049404 restraints weight = 7981.418| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6002 Z= 0.188 Angle : 0.604 8.283 8274 Z= 0.300 Chirality : 0.043 0.148 991 Planarity : 0.003 0.034 1056 Dihedral : 7.831 140.603 941 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.13 % Allowed : 20.22 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.73 (0.30), residues: 843 helix: 1.08 (0.36), residues: 221 sheet: -0.83 (0.31), residues: 268 loop : -1.13 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 19 TYR 0.013 0.001 TYR R 403 PHE 0.023 0.002 PHE L 99 TRP 0.014 0.001 TRP H 106 HIS 0.004 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 ( 5998) covalent geometry : angle 0.60170 / 0.30 ( 8266) SS BOND : bond 0.00289 / 0.13 ( 4) SS BOND : angle 1.71328 / 1.01 ( 8) hydrogen bonds : bond 0.03037 / 2.25 ( 284) hydrogen bonds : angle 5.25706 / 3.88 ( 774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 TYR cc_start: 0.8691 (m-80) cc_final: 0.8487 (m-80) REVERT: R 119 PHE cc_start: 0.8748 (m-10) cc_final: 0.8180 (m-80) REVERT: L 91 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8778 (pp30) outliers start: 19 outliers final: 13 residues processed: 78 average time/residue: 0.0571 time to fit residues: 6.4853 Evaluate side-chains 75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 23 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.065648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046787 restraints weight = 31954.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048217 restraints weight = 16924.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049107 restraints weight = 11511.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.049518 restraints weight = 9097.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049936 restraints weight = 8056.048| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6002 Z= 0.151 Angle : 0.587 7.662 8274 Z= 0.289 Chirality : 0.042 0.148 991 Planarity : 0.003 0.034 1056 Dihedral : 7.780 140.529 941 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.04 % Allowed : 21.74 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.62 (0.30), residues: 843 helix: 1.21 (0.37), residues: 224 sheet: -0.79 (0.31), residues: 267 loop : -1.08 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 7 TYR 0.015 0.001 TYR R 403 PHE 0.024 0.002 PHE L 99 TRP 0.012 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 5998) covalent geometry : angle 0.58490 / 0.29 ( 8266) SS BOND : bond 0.00217 / 0.09 ( 4) SS BOND : angle 1.60422 / 0.95 ( 8) hydrogen bonds : bond 0.02918 / 2.16 ( 284) hydrogen bonds : angle 5.17553 / 3.82 ( 774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 TYR cc_start: 0.8717 (m-80) cc_final: 0.8499 (m-80) REVERT: R 119 PHE cc_start: 0.8720 (m-10) cc_final: 0.8151 (m-80) REVERT: L 24 CYS cc_start: 0.4210 (t) cc_final: 0.3998 (t) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.0626 time to fit residues: 6.5383 Evaluate side-chains 74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.065194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046314 restraints weight = 32133.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047661 restraints weight = 17280.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048572 restraints weight = 11913.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049148 restraints weight = 9438.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049305 restraints weight = 8161.236| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6002 Z= 0.175 Angle : 0.610 9.526 8274 Z= 0.299 Chirality : 0.042 0.145 991 Planarity : 0.003 0.033 1056 Dihedral : 7.808 140.559 941 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.61 % Allowed : 21.96 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.57 (0.30), residues: 843 helix: 1.32 (0.37), residues: 224 sheet: -0.79 (0.31), residues: 267 loop : -1.07 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 25 TYR 0.019 0.001 TYR R 403 PHE 0.019 0.002 PHE L 99 TRP 0.013 0.001 TRP H 106 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 ( 5998) covalent geometry : angle 0.60802 / 0.30 ( 8266) SS BOND : bond 0.00238 / 0.10 ( 4) SS BOND : angle 1.71215 / 1.01 ( 8) hydrogen bonds : bond 0.02960 / 2.19 ( 284) hydrogen bonds : angle 5.24779 / 3.87 ( 774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 104 TYR cc_start: 0.8832 (m-80) cc_final: 0.8609 (m-80) REVERT: R 119 PHE cc_start: 0.8759 (m-10) cc_final: 0.8199 (m-80) REVERT: R 403 TYR cc_start: 0.7133 (t80) cc_final: 0.6689 (t80) outliers start: 12 outliers final: 12 residues processed: 69 average time/residue: 0.0536 time to fit residues: 5.5336 Evaluate side-chains 70 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 55 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.0670 chunk 33 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.0018 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.066520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047726 restraints weight = 31761.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049163 restraints weight = 16747.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050089 restraints weight = 11356.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050683 restraints weight = 8942.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050992 restraints weight = 7693.248| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6002 Z= 0.111 Angle : 0.591 10.276 8274 Z= 0.285 Chirality : 0.043 0.153 991 Planarity : 0.003 0.034 1056 Dihedral : 7.670 140.494 941 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 22.17 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.34 (0.30), residues: 843 helix: 1.67 (0.37), residues: 217 sheet: -0.72 (0.31), residues: 268 loop : -0.93 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 7 TYR 0.017 0.001 TYR R 403 PHE 0.016 0.001 PHE L 99 TRP 0.010 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 5998) covalent geometry : angle 0.58389 / 0.28 ( 8266) SS BOND : bond 0.00345 / 0.17 ( 4) SS BOND : angle 2.92254 / 1.77 ( 8) hydrogen bonds : bond 0.02760 / 2.05 ( 284) hydrogen bonds : angle 4.97937 / 3.67 ( 774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 TYR cc_start: 0.8804 (m-80) cc_final: 0.8528 (m-80) REVERT: R 119 PHE cc_start: 0.8717 (m-10) cc_final: 0.8146 (m-80) REVERT: R 403 TYR cc_start: 0.7164 (t80) cc_final: 0.6841 (t80) REVERT: L 5 MET cc_start: 0.8229 (tpp) cc_final: 0.8028 (tpp) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.0593 time to fit residues: 6.0337 Evaluate side-chains 71 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.064418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045701 restraints weight = 32049.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047022 restraints weight = 17671.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.047891 restraints weight = 12279.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048274 restraints weight = 9783.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048620 restraints weight = 8714.259| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6002 Z= 0.240 Angle : 0.647 10.582 8274 Z= 0.320 Chirality : 0.043 0.141 991 Planarity : 0.004 0.032 1056 Dihedral : 7.830 140.580 941 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.04 % Allowed : 21.96 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.30), residues: 843 helix: 1.55 (0.37), residues: 221 sheet: -0.83 (0.32), residues: 257 loop : -1.01 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 282 TYR 0.018 0.002 TYR R 403 PHE 0.019 0.002 PHE H 105 TRP 0.024 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 ( 5998) covalent geometry : angle 0.64003 / 0.32 ( 8266) SS BOND : bond 0.00707 / 0.35 ( 4) SS BOND : angle 3.19658 / 1.93 ( 8) hydrogen bonds : bond 0.03114 / 2.29 ( 284) hydrogen bonds : angle 5.35031 / 3.94 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1181.40 seconds wall clock time: 21 minutes 5.74 seconds (1265.74 seconds total)