Starting phenix.real_space_refine on Tue Mar 3 14:36:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u1n_20612/03_2026/6u1n_20612.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u1n_20612/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2026/6u1n_20612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2026/6u1n_20612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2026/6u1n_20612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u1n_20612/03_2026/6u1n_20612.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.22, per 1000 atoms: 0.21 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: 0.62 Conformation dependent library (CDL) restraints added in 379.9 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: 0.23 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: 0.88 Time building geometry restraints manager: 0.83 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: 59 58.21 - 87.32: 5 87.32 - 116.42: 0 116.42 - 145.53: 1 Dihedral angle restraints: 3506 sinusoidal: 978 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 3503 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.900 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 12.150 145.527 1862 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 covalent geometry : bond 0.00831 ( 5998) covalent geometry : angle 0.80788 ( 8266) SS BOND : bond 0.00558 ( 4) SS BOND : angle 1.61482 ( 8) hydrogen bonds : bond 0.23020 ( 284) hydrogen bonds : angle 9.34898 ( 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 : 0.241 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: 0.0700 time to fit residues: 7.5873 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 : 0.188 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.063586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.045071 restraints weight = 32684.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046430 restraints weight = 17839.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047285 restraints weight = 12297.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.047799 restraints weight = 9772.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048071 restraints weight = 8545.522| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1508 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= 0.222 Angle : 0.615 7.736 8274 Z= 0.320 Chirality : 0.044 0.165 991 Planarity : 0.004 0.037 1056 Dihedral : 8.594 140.816 942 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.83 % Allowed : 15.43 % 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: -3.27 (0.26), residues: 843 helix: -1.67 (0.31), residues: 217 sheet: -1.96 (0.29), residues: 267 loop : -2.52 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 76 TYR 0.013 0.001 TYR R 131 PHE 0.017 0.002 PHE H 105 TRP 0.018 0.002 TRP H 106 HIS 0.003 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5998) covalent geometry : angle 0.61373 ( 8266) SS BOND : bond 0.00496 ( 4) SS BOND : angle 1.20422 ( 8) hydrogen bonds : bond 0.04192 ( 284) hydrogen bonds : angle 6.47796 ( 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 80 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8876 (m-80) cc_final: 0.8274 (m-80) REVERT: R 397 ILE cc_start: 0.9500 (mt) cc_final: 0.9279 (pt) REVERT: C 256 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8130 (tm-30) REVERT: H 16 GLN cc_start: 0.8336 (mm110) cc_final: 0.8084 (mm-40) REVERT: L 22 ILE cc_start: 0.9461 (mm) cc_final: 0.9244 (mt) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.0598 time to fit residues: 6.7774 Evaluate side-chains 67 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 73 optimal weight: 0.0020 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN H 16 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.063920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045283 restraints weight = 32044.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.046613 restraints weight = 17542.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047469 restraints weight = 12203.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047848 restraints weight = 9693.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048257 restraints weight = 8622.195| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6002 Z= 0.207 Angle : 0.600 8.042 8274 Z= 0.306 Chirality : 0.044 0.170 991 Planarity : 0.004 0.028 1056 Dihedral : 8.444 140.519 942 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.57 % Allowed : 16.52 % Favored : 78.91 % 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: -2.35 (0.28), residues: 843 helix: -0.63 (0.35), residues: 217 sheet: -1.56 (0.29), residues: 273 loop : -2.02 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 76 TYR 0.016 0.002 TYR R 131 PHE 0.017 0.002 PHE H 105 TRP 0.016 0.002 TRP R 155 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5998) covalent geometry : angle 0.59878 ( 8266) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.27314 ( 8) hydrogen bonds : bond 0.03621 ( 284) hydrogen bonds : angle 6.05498 ( 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 87 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8836 (m-10) cc_final: 0.8284 (m-80) REVERT: H 16 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8064 (mm-40) outliers start: 21 outliers final: 12 residues processed: 84 average time/residue: 0.0588 time to fit residues: 6.8560 Evaluate side-chains 72 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 0.0050 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.066425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047803 restraints weight = 31236.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049258 restraints weight = 16430.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050177 restraints weight = 11129.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050765 restraints weight = 8722.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051056 restraints weight = 7510.087| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2720 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= 0.102 Angle : 0.581 9.609 8274 Z= 0.286 Chirality : 0.043 0.163 991 Planarity : 0.003 0.028 1056 Dihedral : 8.058 140.598 942 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.04 % Allowed : 17.17 % Favored : 79.78 % 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: -1.45 (0.29), residues: 843 helix: 0.11 (0.36), residues: 222 sheet: -1.12 (0.32), residues: 261 loop : -1.41 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 7 TYR 0.010 0.001 TYR R 403 PHE 0.011 0.001 PHE H 105 TRP 0.013 0.001 TRP R 155 HIS 0.003 0.001 HIS C 210 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 5998) covalent geometry : angle 0.57717 ( 8266) SS BOND : bond 0.00342 ( 4) SS BOND : angle 2.21292 ( 8) hydrogen bonds : bond 0.03129 ( 284) hydrogen bonds : angle 5.38904 ( 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 84 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8734 (m-10) cc_final: 0.8150 (m-80) REVERT: C 256 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7925 (tm-30) REVERT: L 99 PHE cc_start: 0.8979 (m-80) cc_final: 0.8514 (m-80) REVERT: L 107 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8110 (tp) outliers start: 14 outliers final: 6 residues processed: 83 average time/residue: 0.0639 time to fit residues: 7.3801 Evaluate side-chains 72 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 104 LEU 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 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: 5.9990 chunk 72 optimal weight: 0.0060 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3473 r_free = 0.3473 target = 0.065031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046258 restraints weight = 32309.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047658 restraints weight = 17110.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048547 restraints weight = 11636.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048953 restraints weight = 9188.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049331 restraints weight = 8143.133| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6002 Z= 0.169 Angle : 0.593 7.927 8274 Z= 0.294 Chirality : 0.043 0.152 991 Planarity : 0.003 0.030 1056 Dihedral : 8.123 140.633 942 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.91 % Allowed : 18.70 % Favored : 77.39 % 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: -1.17 (0.30), residues: 843 helix: 0.59 (0.37), residues: 216 sheet: -1.02 (0.32), residues: 252 loop : -1.33 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 19 TYR 0.008 0.001 TYR L 50 PHE 0.018 0.002 PHE H 105 TRP 0.013 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5998) covalent geometry : angle 0.59032 ( 8266) SS BOND : bond 0.00516 ( 4) SS BOND : angle 1.98360 ( 8) hydrogen bonds : bond 0.03173 ( 284) hydrogen bonds : angle 5.36970 ( 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: 18 poor density : 67 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8756 (m-10) cc_final: 0.8167 (m-80) REVERT: H 16 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8003 (mm-40) REVERT: L 99 PHE cc_start: 0.8750 (m-80) cc_final: 0.8496 (m-80) REVERT: L 107 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8089 (tp) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.0509 time to fit residues: 5.9999 Evaluate side-chains 78 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 55 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.066659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.048024 restraints weight = 32179.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049463 restraints weight = 17233.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050368 restraints weight = 11760.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050947 restraints weight = 9296.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051183 restraints weight = 8026.832| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3096 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= 0.102 Angle : 0.579 10.194 8274 Z= 0.278 Chirality : 0.043 0.150 991 Planarity : 0.003 0.030 1056 Dihedral : 7.930 140.568 942 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.13 % Allowed : 19.57 % Favored : 76.30 % 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: -0.78 (0.30), residues: 843 helix: 0.90 (0.37), residues: 221 sheet: -0.84 (0.32), residues: 259 loop : -1.05 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 7 TYR 0.008 0.001 TYR H 107 PHE 0.016 0.001 PHE H 30 TRP 0.012 0.001 TRP R 155 HIS 0.004 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5998) covalent geometry : angle 0.57848 ( 8266) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.06758 ( 8) hydrogen bonds : bond 0.02887 ( 284) hydrogen bonds : angle 5.03993 ( 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 90 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8754 (m-10) cc_final: 0.8159 (m-80) REVERT: C 256 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7691 (tm-30) REVERT: H 16 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8162 (mm-40) REVERT: L 107 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8156 (tp) outliers start: 19 outliers final: 11 residues processed: 86 average time/residue: 0.0581 time to fit residues: 7.1661 Evaluate side-chains 79 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR 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: 10.0000 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3440 r_free = 0.3440 target = 0.063558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044911 restraints weight = 32723.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.046235 restraints weight = 17891.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047056 restraints weight = 12382.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047578 restraints weight = 9884.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047820 restraints weight = 8630.528| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6002 Z= 0.299 Angle : 0.670 6.973 8274 Z= 0.339 Chirality : 0.044 0.150 991 Planarity : 0.004 0.027 1056 Dihedral : 8.314 140.566 942 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.35 % Allowed : 20.00 % 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: -0.99 (0.29), residues: 843 helix: 0.80 (0.36), residues: 224 sheet: -1.00 (0.32), residues: 252 loop : -1.23 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 19 TYR 0.012 0.002 TYR L 50 PHE 0.025 0.003 PHE L 99 TRP 0.023 0.002 TRP H 106 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 5998) covalent geometry : angle 0.66636 ( 8266) SS BOND : bond 0.00428 ( 4) SS BOND : angle 2.20659 ( 8) hydrogen bonds : bond 0.03533 ( 284) hydrogen bonds : angle 5.69228 ( 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 81 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8803 (m-10) cc_final: 0.8268 (m-80) outliers start: 20 outliers final: 16 residues processed: 77 average time/residue: 0.0513 time to fit residues: 5.8158 Evaluate side-chains 74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 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 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 98 THR 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: 20.0000 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 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 = 0.3497 r_free = 0.3497 target = 0.065777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.046982 restraints weight = 32006.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048376 restraints weight = 16921.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049329 restraints weight = 11529.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049884 restraints weight = 9059.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050264 restraints weight = 7852.410| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6002 Z= 0.121 Angle : 0.614 9.881 8274 Z= 0.293 Chirality : 0.043 0.149 991 Planarity : 0.003 0.031 1056 Dihedral : 8.028 140.448 942 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.83 % Allowed : 23.04 % Favored : 74.13 % 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: -0.63 (0.30), residues: 843 helix: 1.20 (0.37), residues: 224 sheet: -0.87 (0.31), residues: 267 loop : -1.01 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 7 TYR 0.011 0.001 TYR R 403 PHE 0.018 0.001 PHE L 99 TRP 0.014 0.001 TRP R 155 HIS 0.004 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5998) covalent geometry : angle 0.61195 ( 8266) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.59854 ( 8) hydrogen bonds : bond 0.02947 ( 284) hydrogen bonds : angle 5.23152 ( 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 79 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8737 (m-10) cc_final: 0.8150 (m-80) REVERT: C 256 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7706 (tm-30) REVERT: H 15 VAL cc_start: 0.9138 (t) cc_final: 0.8838 (m) REVERT: L 24 CYS cc_start: 0.4434 (t) cc_final: 0.4200 (t) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.0599 time to fit residues: 6.5592 Evaluate side-chains 75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 61 optimal weight: 0.0020 chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3468 r_free = 0.3468 target = 0.064796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.045999 restraints weight = 31905.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047411 restraints weight = 17335.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048299 restraints weight = 11801.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048699 restraints weight = 9320.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049145 restraints weight = 8276.219| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3137 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= 0.192 Angle : 0.620 9.063 8274 Z= 0.304 Chirality : 0.043 0.145 991 Planarity : 0.004 0.030 1056 Dihedral : 8.097 140.587 942 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.39 % Allowed : 23.04 % Favored : 74.57 % 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: -0.63 (0.30), residues: 843 helix: 1.27 (0.37), residues: 224 sheet: -0.88 (0.31), residues: 267 loop : -1.05 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 25 TYR 0.018 0.001 TYR R 403 PHE 0.019 0.002 PHE H 105 TRP 0.016 0.001 TRP H 106 HIS 0.003 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5998) covalent geometry : angle 0.61758 ( 8266) SS BOND : bond 0.00367 ( 4) SS BOND : angle 1.87951 ( 8) hydrogen bonds : bond 0.03097 ( 284) hydrogen bonds : angle 5.36939 ( 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 74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8773 (m-10) cc_final: 0.8208 (m-80) REVERT: L 24 CYS cc_start: 0.4193 (t) cc_final: 0.3648 (t) outliers start: 11 outliers final: 11 residues processed: 72 average time/residue: 0.0534 time to fit residues: 5.7119 Evaluate side-chains 74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 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 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: 2.9990 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3480 r_free = 0.3480 target = 0.065108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046236 restraints weight = 32149.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047585 restraints weight = 17260.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048513 restraints weight = 11857.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049102 restraints weight = 9342.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049457 restraints weight = 8065.191| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6002 Z= 0.175 Angle : 0.632 10.751 8274 Z= 0.306 Chirality : 0.043 0.148 991 Planarity : 0.004 0.031 1056 Dihedral : 8.042 140.481 942 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.61 % Allowed : 23.48 % Favored : 73.91 % 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: -0.54 (0.30), residues: 843 helix: 1.38 (0.37), residues: 224 sheet: -0.86 (0.31), residues: 270 loop : -0.98 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 25 TYR 0.020 0.001 TYR R 403 PHE 0.018 0.002 PHE H 105 TRP 0.013 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 5998) covalent geometry : angle 0.62994 ( 8266) SS BOND : bond 0.00352 ( 4) SS BOND : angle 1.66702 ( 8) hydrogen bonds : bond 0.03037 ( 284) hydrogen bonds : angle 5.33377 ( 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 75 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8751 (m-10) cc_final: 0.8174 (m-80) REVERT: L 24 CYS cc_start: 0.4496 (t) cc_final: 0.3940 (t) outliers start: 12 outliers final: 12 residues processed: 73 average time/residue: 0.0512 time to fit residues: 5.5905 Evaluate side-chains 74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 H residue 106 TRP Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL 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 58 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 208 HIS ** L 91 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 = 0.3431 r_free = 0.3431 target = 0.063157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044464 restraints weight = 32646.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045766 restraints weight = 17773.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046617 restraints weight = 12258.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047163 restraints weight = 9738.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047392 restraints weight = 8458.188| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 6002 Z= 0.326 Angle : 0.703 8.824 8274 Z= 0.357 Chirality : 0.044 0.146 991 Planarity : 0.004 0.030 1056 Dihedral : 8.310 140.492 942 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.04 % Allowed : 23.26 % Favored : 73.70 % 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: -0.86 (0.29), residues: 843 helix: 1.07 (0.37), residues: 224 sheet: -1.01 (0.33), residues: 247 loop : -1.20 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 25 TYR 0.026 0.002 TYR R 403 PHE 0.024 0.003 PHE H 105 TRP 0.025 0.002 TRP H 106 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 5998) covalent geometry : angle 0.70051 ( 8266) SS BOND : bond 0.00606 ( 4) SS BOND : angle 2.14413 ( 8) hydrogen bonds : bond 0.03639 ( 284) hydrogen bonds : angle 5.83642 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.72 seconds wall clock time: 19 minutes 40.31 seconds (1180.31 seconds total)