Starting phenix.real_space_refine on Sun Apr 27 16:21:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u1n_20612/04_2025/6u1n_20612.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u1n_20612/04_2025/6u1n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6u1n_20612/04_2025/6u1n_20612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u1n_20612/04_2025/6u1n_20612.map" model { file = "/net/cci-nas-00/data/ceres_data/6u1n_20612/04_2025/6u1n_20612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u1n_20612/04_2025/6u1n_20612.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 13, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLN:plan1': 3, 'ASP:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} 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, 'GLU:plan': 2, 'ASP: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: 4.12, per 1000 atoms: 0.70 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: 1.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.80 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: 2.01 Time building geometry restraints manager: 2.06 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: 23.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.140 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.040 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 PHE 0.020 0.002 PHE H 105 TYR 0.012 0.001 TYR L 50 ARG 0.006 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.23020 ( 284) hydrogen bonds : angle 9.34898 ( 774) SS BOND : bond 0.00558 ( 4) SS BOND : angle 1.61482 ( 8) covalent geometry : bond 0.00831 ( 5998) covalent geometry : angle 0.80788 ( 8266) *********************** 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 : 0.684 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: 0.8461 (m-80) 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: 0.1735 time to fit residues: 18.7456 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 H 16 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.065336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.046677 restraints weight = 31823.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048106 restraints weight = 17046.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049017 restraints weight = 11644.580| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6002 Z= 0.137 Angle : 0.581 6.494 8274 Z= 0.298 Chirality : 0.044 0.169 991 Planarity : 0.004 0.031 1056 Dihedral : 8.393 141.090 942 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.61 % Allowed : 15.00 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.26), residues: 843 helix: -1.40 (0.32), residues: 217 sheet: -1.81 (0.29), residues: 267 loop : -2.31 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 207 HIS 0.002 0.001 HIS C 30 PHE 0.018 0.001 PHE H 30 TYR 0.016 0.001 TYR R 131 ARG 0.005 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 284) hydrogen bonds : angle 6.15550 ( 774) SS BOND : bond 0.00404 ( 4) SS BOND : angle 1.14068 ( 8) covalent geometry : bond 0.00276 ( 5998) covalent geometry : angle 0.57976 ( 8266) *********************** 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 85 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8833 (m-80) cc_final: 0.8235 (m-80) REVERT: R 397 ILE cc_start: 0.9495 (mt) cc_final: 0.9270 (pt) REVERT: C 144 TYR cc_start: 0.8181 (m-80) cc_final: 0.7978 (m-80) REVERT: H 16 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8064 (mm-40) REVERT: L 22 ILE cc_start: 0.9430 (mm) cc_final: 0.9208 (mt) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.1585 time to fit residues: 18.5839 Evaluate side-chains 70 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN ** L 90 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 = 0.3493 r_free = 0.3493 target = 0.065717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046900 restraints weight = 31686.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048359 restraints weight = 16708.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049298 restraints weight = 11329.174| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6002 Z= 0.128 Angle : 0.562 8.552 8274 Z= 0.282 Chirality : 0.043 0.172 991 Planarity : 0.003 0.028 1056 Dihedral : 8.146 140.579 942 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.48 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.28), residues: 843 helix: -0.32 (0.35), residues: 216 sheet: -1.39 (0.31), residues: 261 loop : -1.72 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 PHE 0.015 0.001 PHE H 105 TYR 0.013 0.001 TYR R 104 ARG 0.004 0.001 ARG R 121 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 284) hydrogen bonds : angle 5.69598 ( 774) SS BOND : bond 0.00736 ( 4) SS BOND : angle 1.16348 ( 8) covalent geometry : bond 0.00267 ( 5998) covalent geometry : angle 0.56129 ( 8266) *********************** 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: 16 poor density : 69 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8778 (m-80) cc_final: 0.8204 (m-80) REVERT: R 400 TRP cc_start: 0.7449 (m100) cc_final: 0.7031 (m100) REVERT: C 144 TYR cc_start: 0.8505 (m-80) cc_final: 0.8209 (m-80) REVERT: H 16 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8043 (mm-40) REVERT: L 22 ILE cc_start: 0.9442 (mm) cc_final: 0.9240 (mt) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.1511 time to fit residues: 17.6042 Evaluate side-chains 74 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.063252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.044594 restraints weight = 32775.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045924 restraints weight = 17990.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046753 restraints weight = 12401.024| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6002 Z= 0.289 Angle : 0.652 7.529 8274 Z= 0.334 Chirality : 0.044 0.161 991 Planarity : 0.004 0.028 1056 Dihedral : 8.397 140.574 942 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.35 % Allowed : 17.61 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.29), residues: 843 helix: -0.00 (0.36), residues: 218 sheet: -1.25 (0.32), residues: 252 loop : -1.72 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 106 HIS 0.004 0.001 HIS C 353 PHE 0.021 0.002 PHE H 105 TYR 0.012 0.002 TYR L 50 ARG 0.004 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 284) hydrogen bonds : angle 5.94945 ( 774) SS BOND : bond 0.00528 ( 4) SS BOND : angle 2.76094 ( 8) covalent geometry : bond 0.00600 ( 5998) covalent geometry : angle 0.64707 ( 8266) *********************** 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 82 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8792 (m-10) cc_final: 0.8222 (m-80) REVERT: H 16 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8122 (mm-40) REVERT: L 107 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8102 (tp) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.1316 time to fit residues: 15.7106 Evaluate side-chains 73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 8 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.065677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047065 restraints weight = 31488.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048497 restraints weight = 16738.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049402 restraints weight = 11385.497| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6002 Z= 0.113 Angle : 0.582 9.422 8274 Z= 0.284 Chirality : 0.043 0.155 991 Planarity : 0.003 0.030 1056 Dihedral : 8.066 140.524 942 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.83 % Allowed : 20.00 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.30), residues: 843 helix: 0.43 (0.36), residues: 224 sheet: -1.00 (0.33), residues: 250 loop : -1.28 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 155 HIS 0.002 0.001 HIS C 353 PHE 0.012 0.001 PHE H 105 TYR 0.009 0.001 TYR R 403 ARG 0.003 0.000 ARG C 7 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 284) hydrogen bonds : angle 5.35476 ( 774) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.96804 ( 8) covalent geometry : bond 0.00237 ( 5998) covalent geometry : angle 0.57868 ( 8266) *********************** 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 80 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8712 (m-10) cc_final: 0.8111 (m-80) REVERT: C 256 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7836 (tm-30) REVERT: L 5 MET cc_start: 0.8599 (tpp) cc_final: 0.8338 (tpp) REVERT: L 99 PHE cc_start: 0.8977 (m-80) cc_final: 0.8602 (m-80) outliers start: 13 outliers final: 10 residues processed: 77 average time/residue: 0.1545 time to fit residues: 17.1831 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 : 0.703 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 64 optimal weight: 7.9990 chunk 60 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.065225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046531 restraints weight = 31620.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047924 restraints weight = 16810.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048581 restraints weight = 11470.829| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6002 Z= 0.147 Angle : 0.549 6.537 8274 Z= 0.275 Chirality : 0.042 0.149 991 Planarity : 0.003 0.030 1056 Dihedral : 8.051 140.616 942 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.30), residues: 843 helix: 0.79 (0.36), residues: 224 sheet: -0.93 (0.32), residues: 257 loop : -1.16 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 PHE 0.016 0.001 PHE H 105 TYR 0.007 0.001 TYR L 50 ARG 0.002 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 284) hydrogen bonds : angle 5.28761 ( 774) SS BOND : bond 0.00302 ( 4) SS BOND : angle 1.22770 ( 8) covalent geometry : bond 0.00308 ( 5998) covalent geometry : angle 0.54783 ( 8266) *********************** 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 80 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8708 (m-10) cc_final: 0.8131 (m-80) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.1414 time to fit residues: 15.2764 Evaluate side-chains 73 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.065865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047167 restraints weight = 31840.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048600 restraints weight = 16869.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049503 restraints weight = 11457.184| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6002 Z= 0.128 Angle : 0.579 10.310 8274 Z= 0.282 Chirality : 0.042 0.147 991 Planarity : 0.003 0.030 1056 Dihedral : 7.956 140.539 942 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.13 % Allowed : 20.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.30), residues: 843 helix: 1.05 (0.36), residues: 224 sheet: -0.85 (0.32), residues: 257 loop : -1.06 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 155 HIS 0.004 0.001 HIS C 353 PHE 0.025 0.002 PHE L 99 TYR 0.007 0.001 TYR R 403 ARG 0.002 0.000 ARG C 7 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 284) hydrogen bonds : angle 5.15907 ( 774) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.39186 ( 8) covalent geometry : bond 0.00271 ( 5998) covalent geometry : angle 0.57739 ( 8266) *********************** 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 83 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8726 (m-10) cc_final: 0.8139 (m-80) REVERT: C 256 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7749 (tm-30) REVERT: L 24 CYS cc_start: 0.4259 (t) cc_final: 0.4002 (t) REVERT: L 99 PHE cc_start: 0.8759 (m-80) cc_final: 0.8486 (m-10) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 0.1282 time to fit residues: 14.8102 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 : 0.623 ------------------------------------------------------------------------------- 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 150 VAL Chi-restraints excluded: chain C residue 186 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN ** 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 = 0.3510 r_free = 0.3510 target = 0.066463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.047729 restraints weight = 31574.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049187 restraints weight = 16677.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050104 restraints weight = 11294.381| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6002 Z= 0.110 Angle : 0.567 8.621 8274 Z= 0.276 Chirality : 0.042 0.142 991 Planarity : 0.003 0.031 1056 Dihedral : 7.841 140.565 942 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.83 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 843 helix: 1.44 (0.37), residues: 217 sheet: -0.76 (0.32), residues: 260 loop : -0.94 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 155 HIS 0.003 0.001 HIS C 353 PHE 0.015 0.001 PHE L 99 TYR 0.015 0.001 TYR R 403 ARG 0.002 0.000 ARG C 7 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 284) hydrogen bonds : angle 4.97995 ( 774) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.30483 ( 8) covalent geometry : bond 0.00234 ( 5998) covalent geometry : angle 0.56566 ( 8266) *********************** 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 78 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8731 (m-10) cc_final: 0.8143 (m-80) REVERT: H 15 VAL cc_start: 0.9128 (t) cc_final: 0.8812 (m) REVERT: L 24 CYS cc_start: 0.4765 (t) cc_final: 0.4562 (t) outliers start: 13 outliers final: 13 residues processed: 74 average time/residue: 0.1561 time to fit residues: 16.3256 Evaluate side-chains 76 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 C residue 317 ILE Chi-restraints excluded: chain H residue 106 TRP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.064891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046255 restraints weight = 32389.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047588 restraints weight = 17588.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.048237 restraints weight = 12157.530| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3215 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= 0.204 Angle : 0.624 8.445 8274 Z= 0.306 Chirality : 0.043 0.147 991 Planarity : 0.004 0.031 1056 Dihedral : 7.994 140.567 942 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.26 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.30), residues: 843 helix: 1.39 (0.37), residues: 224 sheet: -0.76 (0.31), residues: 269 loop : -1.04 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 106 HIS 0.003 0.001 HIS C 353 PHE 0.017 0.002 PHE H 105 TYR 0.015 0.001 TYR R 403 ARG 0.003 0.000 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 284) hydrogen bonds : angle 5.29981 ( 774) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.65048 ( 8) covalent geometry : bond 0.00428 ( 5998) covalent geometry : angle 0.62227 ( 8266) *********************** 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 77 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 PHE cc_start: 0.8729 (m-10) cc_final: 0.8170 (m-80) REVERT: L 24 CYS cc_start: 0.4530 (t) cc_final: 0.4237 (t) outliers start: 15 outliers final: 14 residues processed: 74 average time/residue: 0.1436 time to fit residues: 15.6702 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 : 0.680 ------------------------------------------------------------------------------- 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 C residue 317 ILE Chi-restraints excluded: chain H residue 106 TRP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2067 > 50: distance: 19 - 33: 20.164 distance: 30 - 33: 20.592 distance: 31 - 48: 12.188 distance: 33 - 34: 10.046 distance: 34 - 35: 10.856 distance: 34 - 37: 19.005 distance: 35 - 36: 21.616 distance: 35 - 38: 14.027 distance: 38 - 39: 30.797 distance: 39 - 40: 8.376 distance: 39 - 42: 6.825 distance: 40 - 41: 16.077 distance: 40 - 43: 19.246 distance: 41 - 61: 10.910 distance: 43 - 44: 8.459 distance: 44 - 45: 15.373 distance: 44 - 47: 15.564 distance: 45 - 46: 18.416 distance: 45 - 48: 16.368 distance: 46 - 66: 21.743 distance: 48 - 49: 11.046 distance: 49 - 50: 9.715 distance: 49 - 52: 7.312 distance: 50 - 51: 24.063 distance: 50 - 56: 8.776 distance: 51 - 72: 26.058 distance: 52 - 53: 3.988 distance: 53 - 54: 13.696 distance: 53 - 55: 11.423 distance: 56 - 57: 17.369 distance: 57 - 58: 8.395 distance: 57 - 60: 13.201 distance: 58 - 59: 19.692 distance: 58 - 61: 4.270 distance: 62 - 63: 15.446 distance: 62 - 65: 15.804 distance: 63 - 64: 9.474 distance: 63 - 66: 15.650 distance: 66 - 67: 8.972 distance: 67 - 68: 12.119 distance: 67 - 70: 14.645 distance: 68 - 69: 23.459 distance: 68 - 72: 16.698 distance: 70 - 71: 39.011 distance: 72 - 73: 14.884 distance: 73 - 74: 21.120 distance: 73 - 76: 6.639 distance: 74 - 75: 21.547 distance: 74 - 77: 24.525 distance: 77 - 78: 32.233 distance: 77 - 83: 10.732 distance: 78 - 79: 14.365 distance: 78 - 81: 13.135 distance: 79 - 80: 17.504 distance: 79 - 84: 10.147 distance: 81 - 82: 31.712 distance: 82 - 83: 17.442 distance: 84 - 85: 15.196 distance: 85 - 86: 11.167 distance: 85 - 88: 10.444 distance: 86 - 87: 10.797 distance: 86 - 90: 21.002 distance: 88 - 89: 16.058