Starting phenix.real_space_refine on Thu Aug 6 23:56:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ysg_73392/08_2026/9ysg_73392_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ysg_73392/08_2026/9ysg_73392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ysg_73392/08_2026/9ysg_73392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ysg_73392/08_2026/9ysg_73392.map" model { file = "/net/cci-nas-00/data/ceres_data/9ysg_73392/08_2026/9ysg_73392_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ysg_73392/08_2026/9ysg_73392_trim.cif" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 5587 2.51 5 N 1481 2.21 5 O 1753 1.98 5 H 8518 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17375 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4210 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain: "D" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3371 Classifications: {'peptide': 225} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "E" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3193 Classifications: {'peptide': 212} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3308 Classifications: {'peptide': 220} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3241 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N GLY A 416 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY A 416 " occ=0.00 residue: pdb=" N GLN A 474 " occ=0.00 ... (15 atoms not shown) pdb="HE22 GLN A 474 " occ=0.00 residue: pdb=" N GLN A 564 " occ=0.00 ... (15 atoms not shown) pdb="HE22 GLN A 564 " occ=0.00 Time building chain proxies: 3.05, per 1000 atoms: 0.18 Number of scatterers: 17375 At special positions: 0 Unit cell: (96.416, 103.04, 166.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 1753 8.00 N 1481 7.00 C 5587 6.00 H 8518 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 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 Links applied BETA1-4 " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 701 " - " ASN A 331 " " NAG T 1 " - " ASN A 343 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 529.6 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 27 sheets defined 10.3% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.938A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.659A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.227A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.296A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 185 through 190 removed outlier: 4.230A pdb=" N GLY D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 120 through 127 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.762A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.526A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 removed outlier: 3.516A pdb=" N SER G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.673A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.450A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.547A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.732A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 121 through 124 removed outlier: 3.613A pdb=" N LEU D 124 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 121 through 124 removed outlier: 3.613A pdb=" N LEU D 124 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 150 through 154 Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6 removed outlier: 4.177A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.899A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.899A pdb=" N VAL E 132 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 152 through 153 removed outlier: 3.589A pdb=" N LYS E 144 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.859A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.674A pdb=" N VAL F 108 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 127 through 130 removed outlier: 3.511A pdb=" N GLY F 145 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP F 150 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR F 182 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 127 through 130 removed outlier: 3.511A pdb=" N GLY F 145 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP F 150 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR F 182 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 157 through 160 Processing sheet with id=AC5, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.728A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.845A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 153 through 154 377 hydrogen bonds defined for protein. 897 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: 3.44 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8515 1.03 - 1.23: 9 1.23 - 1.42: 3902 1.42 - 1.62: 5120 1.62 - 1.81: 44 Bond restraints: 17590 Sorted by residual: bond pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.22e+00 bond pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.27e-02 6.20e+03 5.85e+00 bond pdb=" N GLY A 482 " pdb=" H GLY A 482 " ideal model delta sigma weight residual 0.860 0.906 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" N GLY A 485 " pdb=" H GLY A 485 " ideal model delta sigma weight residual 0.860 0.903 -0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" N ASN A 481 " pdb=" H ASN A 481 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 17585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 30523 1.31 - 2.61: 973 2.61 - 3.92: 120 3.92 - 5.22: 21 5.22 - 6.53: 4 Bond angle restraints: 31641 Sorted by residual: angle pdb=" N CYS A 480 " pdb=" CA CYS A 480 " pdb=" CB CYS A 480 " ideal model delta sigma weight residual 109.69 116.22 -6.53 1.59e+00 3.96e-01 1.69e+01 angle pdb=" CA ASN F 161 " pdb=" C ASN F 161 " pdb=" O ASN F 161 " ideal model delta sigma weight residual 121.54 117.07 4.47 1.16e+00 7.43e-01 1.48e+01 angle pdb=" CA LYS A 478 " pdb=" C LYS A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 118.23 121.71 -3.48 9.20e-01 1.18e+00 1.43e+01 angle pdb=" N VAL A 483 " pdb=" CA VAL A 483 " pdb=" C VAL A 483 " ideal model delta sigma weight residual 111.90 108.85 3.05 8.10e-01 1.52e+00 1.42e+01 angle pdb=" CA ALA F 164 " pdb=" C ALA F 164 " pdb=" O ALA F 164 " ideal model delta sigma weight residual 120.51 115.51 5.00 1.43e+00 4.89e-01 1.22e+01 ... (remaining 31636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7656 17.12 - 34.23: 553 34.23 - 51.35: 193 51.35 - 68.46: 89 68.46 - 85.58: 34 Dihedral angle restraints: 8525 sinusoidal: 4589 harmonic: 3936 Sorted by residual: dihedral pdb=" CA LYS D 143 " pdb=" C LYS D 143 " pdb=" N ASP D 144 " pdb=" CA ASP D 144 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual 93.00 55.58 37.42 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CB CYS F 146 " pdb=" SG CYS F 146 " pdb=" SG CYS F 202 " pdb=" CB CYS F 202 " ideal model delta sinusoidal sigma weight residual 93.00 55.96 37.04 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1032 0.040 - 0.080: 213 0.080 - 0.120: 117 0.120 - 0.159: 18 0.159 - 0.199: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA VAL A 483 " pdb=" N VAL A 483 " pdb=" C VAL A 483 " pdb=" CB VAL A 483 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 8.91e-01 chirality pdb=" CA VAL D 184 " pdb=" N VAL D 184 " pdb=" C VAL D 184 " pdb=" CB VAL D 184 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1378 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 481 " 0.110 2.00e-02 2.50e+03 4.37e-01 2.86e+03 pdb=" CG ASN A 481 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 481 " -0.109 2.00e-02 2.50e+03 pdb=" ND2 ASN A 481 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 481 " -0.745 2.00e-02 2.50e+03 pdb="HD22 ASN A 481 " 0.752 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 161 " 0.083 2.00e-02 2.50e+03 8.92e-02 1.19e+02 pdb=" CG ASN F 161 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN F 161 " -0.083 2.00e-02 2.50e+03 pdb=" ND2 ASN F 161 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN F 161 " -0.131 2.00e-02 2.50e+03 pdb="HD22 ASN F 161 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 485 " -0.011 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" N VAL A 486 " 0.035 2.00e-02 2.50e+03 pdb=" CA VAL A 486 " -0.009 2.00e-02 2.50e+03 pdb=" H VAL A 486 " -0.015 2.00e-02 2.50e+03 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 232 2.05 - 2.69: 26460 2.69 - 3.33: 49161 3.33 - 3.96: 65256 3.96 - 4.60: 100628 Nonbonded interactions: 241737 Sorted by model distance: nonbonded pdb=" OE1 GLU E 122 " pdb=" H GLU E 122 " model vdw 1.418 2.450 nonbonded pdb=" OE1 GLU E 81 " pdb=" H GLU E 81 " model vdw 1.429 2.450 nonbonded pdb=" OE1 GLU G 123 " pdb=" H GLU G 123 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLN F 39 " pdb="HE22 GLN G 38 " model vdw 1.600 2.450 nonbonded pdb=" OE1 GLU G 143 " pdb=" H GLU G 143 " model vdw 1.604 2.450 ... (remaining 241732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 1 through 31 or resid 36 through 52A or resid 55 through 5 \ 8 or resid 60 through 61 or resid 63 through 68 or resid 70 through 80 or resid \ 82 through 82C or resid 84 through 92 or resid 94 or resid 96 or resid 100B or r \ esid 100F or resid 101 through 104 or resid 106 through 126 or resid 128 or resi \ d 130 through 132 or resid 135 through 191 or resid 193 through 194 or resid 196 \ through 198 or resid 200 through 209 or resid 211 through 212 or resid 214)) selection = (chain 'F' and (resid 1 through 31 or resid 36 through 53 or resid 56 through 59 \ or resid 61 through 62 or resid 64 through 69 or resid 71 through 81 or resid 8 \ 3 through 86 or resid 88 through 96 or resid 98 through 99 or resid 103 or resid \ 105 or resid 107 through 110 or resid 112 through 132 or resid 134 or resid 136 \ through 138 or resid 141 through 197 or resid 199 through 200 or resid 202 thro \ ugh 204 or resid 206 through 215 or resid 217 through 218 or resid 220)) } ncs_group { reference = (chain 'E' and (resid 1 through 19 or resid 21 through 29 or resid 33 through 38 \ or resid 40 through 83 or resid 85 through 86 or resid 88 through 92 or resid 9 \ 4 or resid 96 through 212)) selection = (chain 'G' and (resid 1 through 19 or resid 21 through 29 or resid 33 through 38 \ or resid 40 through 83 or resid 85 through 86 or resid 88 through 92 or resid 9 \ 4 or resid 97 through 213)) } 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=0.00 max=1.00 mean=0.90 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.000 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9088 Z= 0.153 Angle : 0.611 6.531 12384 Z= 0.352 Chirality : 0.044 0.199 1381 Planarity : 0.004 0.044 1586 Dihedral : 13.560 85.578 3302 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 0.81 % Allowed : 10.75 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: 0.08 (0.26), residues: 1128 helix: -2.09 (0.61), residues: 58 sheet: 0.88 (0.24), residues: 488 loop : -0.40 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 108 TYR 0.010 0.001 TYR E 91 PHE 0.007 0.001 PHE A 375 TRP 0.011 0.001 TRP F 50 HIS 0.002 0.001 HIS F 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 9072) covalent geometry : angle 0.60692 / 0.35 (12348) SS BOND : bond 0.00128 / 0.07 ( 12) SS BOND : angle 1.03897 / 0.63 ( 24) hydrogen bonds : bond 0.21477 / 13.97 ( 333) hydrogen bonds : angle 9.46284 / 6.43 ( 897) link_BETA1-4 : bond 0.00187 / 0.10 ( 1) link_BETA1-4 : angle 2.31208 / 1.15 ( 3) link_BETA1-6 : bond 0.00890 / 0.47 ( 1) link_BETA1-6 : angle 1.36235 / 0.78 ( 3) link_NAG-ASN : bond 0.00413 / 0.20 ( 2) link_NAG-ASN : angle 1.83421 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 85 ASP cc_start: 0.9482 (t0) cc_final: 0.9264 (t0) REVERT: D 144 ASP cc_start: 0.8703 (p0) cc_final: 0.8428 (p0) REVERT: D 146 PHE cc_start: 0.7468 (t80) cc_final: 0.7231 (t80) REVERT: D 171 GLN cc_start: 0.7600 (mt0) cc_final: 0.7164 (mt0) REVERT: E 47 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (pp) REVERT: E 157 ASN cc_start: 0.9160 (m110) cc_final: 0.8337 (t0) REVERT: F 154 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7891 (tp30) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.7351 time to fit residues: 47.6083 Evaluate side-chains 53 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 128 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.102589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070976 restraints weight = 55882.726| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.84 r_work: 0.3088 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1533 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1534 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9088 Z= 0.219 Angle : 0.585 7.333 12384 Z= 0.307 Chirality : 0.046 0.168 1381 Planarity : 0.004 0.055 1586 Dihedral : 5.615 51.970 1319 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.44 % Rotamer: Outliers : 1.22 % Allowed : 9.74 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.16 (0.26), residues: 1128 helix: -2.21 (0.61), residues: 58 sheet: 0.63 (0.24), residues: 496 loop : -0.49 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 328 TYR 0.015 0.001 TYR E 91 PHE 0.012 0.001 PHE G 73 TRP 0.011 0.001 TRP F 50 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 ( 9072) covalent geometry : angle 0.58190 / 0.31 (12348) SS BOND : bond 0.00424 / 0.23 ( 12) SS BOND : angle 0.81126 / 0.52 ( 24) hydrogen bonds : bond 0.04398 / 2.83 ( 333) hydrogen bonds : angle 6.87706 / 4.62 ( 897) link_BETA1-4 : bond 0.00003 / 0.00 ( 1) link_BETA1-4 : angle 2.13254 / 1.04 ( 3) link_BETA1-6 : bond 0.00321 / 0.17 ( 1) link_BETA1-6 : angle 1.55252 / 0.86 ( 3) link_NAG-ASN : bond 0.00235 / 0.12 ( 2) link_NAG-ASN : angle 1.65389 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6915 (pm20) cc_final: 0.4796 (pm20) REVERT: D 146 PHE cc_start: 0.7571 (t80) cc_final: 0.7353 (t80) REVERT: D 171 GLN cc_start: 0.7722 (mt0) cc_final: 0.7233 (mt0) REVERT: E 47 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8359 (pp) REVERT: E 104 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: E 122 GLU cc_start: 0.8922 (mp0) cc_final: 0.8685 (mp0) REVERT: E 157 ASN cc_start: 0.9161 (m110) cc_final: 0.8348 (t0) REVERT: E 164 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: F 154 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7876 (tp30) outliers start: 12 outliers final: 4 residues processed: 59 average time/residue: 0.8053 time to fit residues: 52.2403 Evaluate side-chains 55 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.102020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069681 restraints weight = 56430.788| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.93 r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1534 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1535 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9088 Z= 0.201 Angle : 0.549 5.549 12384 Z= 0.286 Chirality : 0.045 0.150 1381 Planarity : 0.004 0.055 1586 Dihedral : 5.478 51.075 1317 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 1.83 % Allowed : 9.43 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.26 (0.26), residues: 1128 helix: -2.03 (0.62), residues: 58 sheet: 0.54 (0.24), residues: 485 loop : -0.55 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 38 TYR 0.014 0.001 TYR E 91 PHE 0.011 0.001 PHE E 73 TRP 0.010 0.001 TRP F 50 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 9072) covalent geometry : angle 0.54596 / 0.29 (12348) SS BOND : bond 0.00247 / 0.14 ( 12) SS BOND : angle 0.82664 / 0.51 ( 24) hydrogen bonds : bond 0.03854 / 2.46 ( 333) hydrogen bonds : angle 6.24715 / 4.19 ( 897) link_BETA1-4 : bond 0.00050 / 0.03 ( 1) link_BETA1-4 : angle 2.06787 / 1.01 ( 3) link_BETA1-6 : bond 0.00363 / 0.19 ( 1) link_BETA1-6 : angle 1.52099 / 0.84 ( 3) link_NAG-ASN : bond 0.00166 / 0.08 ( 2) link_NAG-ASN : angle 1.52567 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6891 (pm20) cc_final: 0.4947 (pm20) REVERT: D 146 PHE cc_start: 0.7586 (t80) cc_final: 0.7378 (t80) REVERT: D 171 GLN cc_start: 0.7804 (mt0) cc_final: 0.7258 (mt0) REVERT: E 104 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: E 122 GLU cc_start: 0.8981 (mp0) cc_final: 0.8645 (mp0) REVERT: E 157 ASN cc_start: 0.9147 (m110) cc_final: 0.8406 (t0) REVERT: E 164 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: F 154 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7949 (tp30) outliers start: 18 outliers final: 6 residues processed: 63 average time/residue: 0.7403 time to fit residues: 51.6036 Evaluate side-chains 56 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 214 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN F 170 HIS G 189 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.103400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071865 restraints weight = 56387.459| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.81 r_work: 0.3111 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1535 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1536 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9088 Z= 0.140 Angle : 0.531 5.527 12384 Z= 0.274 Chirality : 0.045 0.144 1381 Planarity : 0.004 0.056 1586 Dihedral : 5.335 51.624 1315 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 1.32 % Allowed : 9.74 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.23 (0.26), residues: 1128 helix: -1.36 (0.71), residues: 51 sheet: 0.45 (0.23), residues: 501 loop : -0.53 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 38 TYR 0.012 0.001 TYR E 91 PHE 0.008 0.001 PHE G 73 TRP 0.009 0.001 TRP F 50 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9072) covalent geometry : angle 0.52889 / 0.27 (12348) SS BOND : bond 0.00291 / 0.16 ( 12) SS BOND : angle 0.72185 / 0.45 ( 24) hydrogen bonds : bond 0.03219 / 2.06 ( 333) hydrogen bonds : angle 5.88581 / 3.94 ( 897) link_BETA1-4 : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : angle 1.80557 / 0.88 ( 3) link_BETA1-6 : bond 0.00318 / 0.17 ( 1) link_BETA1-6 : angle 1.35347 / 0.75 ( 3) link_NAG-ASN : bond 0.00276 / 0.13 ( 2) link_NAG-ASN : angle 1.42455 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6708 (pm20) cc_final: 0.4912 (pm20) REVERT: D 144 ASP cc_start: 0.8948 (p0) cc_final: 0.8733 (p0) REVERT: D 171 GLN cc_start: 0.7804 (mt0) cc_final: 0.7279 (mt0) REVERT: E 31 ASP cc_start: 0.8283 (t70) cc_final: 0.7937 (t0) REVERT: E 47 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8441 (pp) REVERT: E 104 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: E 122 GLU cc_start: 0.8999 (mp0) cc_final: 0.8645 (mp0) REVERT: E 157 ASN cc_start: 0.9145 (m110) cc_final: 0.8436 (t0) REVERT: E 164 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8457 (tp30) REVERT: F 73 ASP cc_start: 0.8731 (t0) cc_final: 0.8303 (t70) REVERT: F 154 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7911 (tp30) REVERT: F 218 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.7687 time to fit residues: 54.0549 Evaluate side-chains 62 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 214 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.103472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072073 restraints weight = 55982.224| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.79 r_work: 0.3113 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1536 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1542 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9088 Z= 0.135 Angle : 0.523 5.524 12384 Z= 0.270 Chirality : 0.044 0.140 1381 Planarity : 0.004 0.056 1586 Dihedral : 5.254 52.372 1315 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 1.62 % Allowed : 10.04 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.24 (0.26), residues: 1128 helix: -1.12 (0.73), residues: 51 sheet: 0.44 (0.23), residues: 501 loop : -0.54 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 94 TYR 0.012 0.001 TYR E 91 PHE 0.020 0.001 PHE D 146 TRP 0.009 0.001 TRP F 50 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 9072) covalent geometry : angle 0.52046 / 0.27 (12348) SS BOND : bond 0.00185 / 0.11 ( 12) SS BOND : angle 0.84647 / 0.52 ( 24) hydrogen bonds : bond 0.03045 / 1.94 ( 333) hydrogen bonds : angle 5.66995 / 3.80 ( 897) link_BETA1-4 : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : angle 1.75139 / 0.85 ( 3) link_BETA1-6 : bond 0.00293 / 0.15 ( 1) link_BETA1-6 : angle 1.37450 / 0.76 ( 3) link_NAG-ASN : bond 0.00216 / 0.10 ( 2) link_NAG-ASN : angle 1.43172 / 0.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6788 (pm20) cc_final: 0.4999 (pm20) REVERT: D 146 PHE cc_start: 0.7464 (t80) cc_final: 0.7213 (t80) REVERT: D 171 GLN cc_start: 0.7817 (mt0) cc_final: 0.7280 (mt0) REVERT: E 31 ASP cc_start: 0.8271 (t0) cc_final: 0.7889 (t0) REVERT: E 104 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: E 122 GLU cc_start: 0.8999 (mp0) cc_final: 0.8621 (mp0) REVERT: E 157 ASN cc_start: 0.9142 (m110) cc_final: 0.8461 (t0) REVERT: E 164 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8462 (tp30) REVERT: F 73 ASP cc_start: 0.8745 (t0) cc_final: 0.8302 (t70) REVERT: F 154 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7899 (tp30) REVERT: F 218 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7964 (tm-30) outliers start: 16 outliers final: 9 residues processed: 65 average time/residue: 0.8133 time to fit residues: 57.9338 Evaluate side-chains 61 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 214 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN F 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.102638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070864 restraints weight = 56383.206| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.83 r_work: 0.3089 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1542 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1548 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9088 Z= 0.204 Angle : 0.545 5.588 12384 Z= 0.282 Chirality : 0.045 0.148 1381 Planarity : 0.004 0.056 1586 Dihedral : 5.344 51.474 1315 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 1.62 % Allowed : 10.24 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.32 (0.26), residues: 1128 helix: -1.00 (0.75), residues: 51 sheet: 0.37 (0.23), residues: 501 loop : -0.62 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 38 TYR 0.014 0.001 TYR E 91 PHE 0.016 0.001 PHE D 146 TRP 0.010 0.001 TRP F 50 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 9072) covalent geometry : angle 0.54261 / 0.28 (12348) SS BOND : bond 0.00234 / 0.13 ( 12) SS BOND : angle 0.81834 / 0.51 ( 24) hydrogen bonds : bond 0.03137 / 2.00 ( 333) hydrogen bonds : angle 5.64359 / 3.78 ( 897) link_BETA1-4 : bond 0.00062 / 0.03 ( 1) link_BETA1-4 : angle 1.93333 / 0.94 ( 3) link_BETA1-6 : bond 0.00260 / 0.14 ( 1) link_BETA1-6 : angle 1.53695 / 0.84 ( 3) link_NAG-ASN : bond 0.00115 / 0.06 ( 2) link_NAG-ASN : angle 1.43754 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6810 (pm20) cc_final: 0.5083 (pm20) REVERT: D 171 GLN cc_start: 0.7838 (mt0) cc_final: 0.7300 (mt0) REVERT: E 31 ASP cc_start: 0.8324 (t0) cc_final: 0.7960 (t0) REVERT: E 104 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: E 122 GLU cc_start: 0.9004 (mp0) cc_final: 0.8599 (mp0) REVERT: E 157 ASN cc_start: 0.9124 (m110) cc_final: 0.8453 (t0) REVERT: E 164 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: F 73 ASP cc_start: 0.8781 (t0) cc_final: 0.8467 (t0) REVERT: F 154 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7905 (tp30) REVERT: F 218 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7495 (tm-30) outliers start: 16 outliers final: 9 residues processed: 62 average time/residue: 0.7953 time to fit residues: 54.1222 Evaluate side-chains 61 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 214 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.103839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072087 restraints weight = 56389.101| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.81 r_work: 0.3130 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1548 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1552 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9088 Z= 0.132 Angle : 0.521 6.449 12384 Z= 0.269 Chirality : 0.044 0.139 1381 Planarity : 0.004 0.056 1586 Dihedral : 5.208 52.250 1315 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 1.42 % Allowed : 10.75 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.31 (0.26), residues: 1128 helix: -0.97 (0.75), residues: 52 sheet: 0.35 (0.23), residues: 504 loop : -0.58 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 509 TYR 0.011 0.001 TYR E 91 PHE 0.018 0.001 PHE D 146 TRP 0.008 0.001 TRP F 50 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9072) covalent geometry : angle 0.51899 / 0.27 (12348) SS BOND : bond 0.00191 / 0.11 ( 12) SS BOND : angle 0.69105 / 0.43 ( 24) hydrogen bonds : bond 0.02860 / 1.83 ( 333) hydrogen bonds : angle 5.41812 / 3.64 ( 897) link_BETA1-4 : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : angle 1.72243 / 0.84 ( 3) link_BETA1-6 : bond 0.00462 / 0.24 ( 1) link_BETA1-6 : angle 1.43217 / 0.79 ( 3) link_NAG-ASN : bond 0.00241 / 0.12 ( 2) link_NAG-ASN : angle 1.36282 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6736 (pm20) cc_final: 0.4950 (pm20) REVERT: D 171 GLN cc_start: 0.7786 (mt0) cc_final: 0.7221 (mt0) REVERT: E 31 ASP cc_start: 0.8192 (t0) cc_final: 0.7781 (t0) REVERT: E 104 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: E 122 GLU cc_start: 0.9017 (mp0) cc_final: 0.8616 (mp0) REVERT: E 157 ASN cc_start: 0.9112 (m110) cc_final: 0.8440 (t0) REVERT: E 164 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: F 73 ASP cc_start: 0.8632 (t0) cc_final: 0.8153 (t70) REVERT: F 154 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7841 (tp30) REVERT: F 218 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7466 (tm-30) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.7665 time to fit residues: 52.0062 Evaluate side-chains 58 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 214 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072398 restraints weight = 56170.288| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.81 r_work: 0.3133 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1553 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9088 Z= 0.118 Angle : 0.513 5.528 12384 Z= 0.264 Chirality : 0.044 0.139 1381 Planarity : 0.004 0.055 1586 Dihedral : 5.100 52.928 1315 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 1.42 % Allowed : 11.05 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.23 (0.26), residues: 1128 helix: -0.88 (0.76), residues: 52 sheet: 0.39 (0.24), residues: 501 loop : -0.51 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.011 0.001 TYR E 91 PHE 0.017 0.001 PHE D 146 TRP 0.009 0.001 TRP F 50 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9072) covalent geometry : angle 0.51128 / 0.26 (12348) SS BOND : bond 0.00171 / 0.10 ( 12) SS BOND : angle 0.63737 / 0.40 ( 24) hydrogen bonds : bond 0.02755 / 1.77 ( 333) hydrogen bonds : angle 5.27371 / 3.55 ( 897) link_BETA1-4 : bond 0.00128 / 0.07 ( 1) link_BETA1-4 : angle 1.61166 / 0.79 ( 3) link_BETA1-6 : bond 0.00312 / 0.16 ( 1) link_BETA1-6 : angle 1.31394 / 0.72 ( 3) link_NAG-ASN : bond 0.00210 / 0.10 ( 2) link_NAG-ASN : angle 1.34652 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6684 (pm20) cc_final: 0.4833 (pm20) REVERT: D 146 PHE cc_start: 0.7310 (t80) cc_final: 0.7102 (t80) REVERT: D 171 GLN cc_start: 0.7900 (mt0) cc_final: 0.7379 (mt0) REVERT: E 31 ASP cc_start: 0.8222 (t0) cc_final: 0.7845 (t0) REVERT: E 104 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: E 122 GLU cc_start: 0.9028 (mp0) cc_final: 0.8614 (mp0) REVERT: E 157 ASN cc_start: 0.9072 (m110) cc_final: 0.8481 (t0) REVERT: E 164 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: F 73 ASP cc_start: 0.8735 (t0) cc_final: 0.8419 (t0) REVERT: F 154 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7875 (tp30) REVERT: F 218 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7452 (tm-30) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.7508 time to fit residues: 50.1050 Evaluate side-chains 60 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 214 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 ASN A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.103415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071616 restraints weight = 56342.521| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.80 r_work: 0.3121 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1553 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1554 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9088 Z= 0.175 Angle : 0.527 5.576 12384 Z= 0.272 Chirality : 0.044 0.146 1381 Planarity : 0.004 0.056 1586 Dihedral : 5.161 51.947 1315 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 1.32 % Allowed : 11.46 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.30 (0.26), residues: 1128 helix: -0.84 (0.76), residues: 52 sheet: 0.33 (0.24), residues: 503 loop : -0.56 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 38 TYR 0.013 0.001 TYR E 91 PHE 0.014 0.001 PHE D 146 TRP 0.009 0.001 TRP F 50 HIS 0.004 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9072) covalent geometry : angle 0.52451 / 0.27 (12348) SS BOND : bond 0.00206 / 0.12 ( 12) SS BOND : angle 0.70730 / 0.44 ( 24) hydrogen bonds : bond 0.02865 / 1.84 ( 333) hydrogen bonds : angle 5.31828 / 3.58 ( 897) link_BETA1-4 : bond 0.00064 / 0.03 ( 1) link_BETA1-4 : angle 1.73931 / 0.85 ( 3) link_BETA1-6 : bond 0.00283 / 0.15 ( 1) link_BETA1-6 : angle 1.48130 / 0.81 ( 3) link_NAG-ASN : bond 0.00094 / 0.05 ( 2) link_NAG-ASN : angle 1.40817 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6821 (pm20) cc_final: 0.5517 (pm20) REVERT: D 171 GLN cc_start: 0.7809 (mt0) cc_final: 0.7254 (mt0) REVERT: E 31 ASP cc_start: 0.8215 (t0) cc_final: 0.7801 (t0) REVERT: E 104 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: E 122 GLU cc_start: 0.9027 (mp0) cc_final: 0.8592 (mp0) REVERT: E 157 ASN cc_start: 0.9080 (m110) cc_final: 0.8463 (t0) REVERT: E 164 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8445 (tp30) REVERT: F 73 ASP cc_start: 0.8665 (t0) cc_final: 0.8298 (t0) REVERT: F 154 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7866 (tp30) REVERT: F 218 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7447 (tm-30) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.8475 time to fit residues: 56.3085 Evaluate side-chains 60 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.103980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072300 restraints weight = 55713.599| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.80 r_work: 0.3135 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1554 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1557 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9088 Z= 0.120 Angle : 0.526 7.522 12384 Z= 0.271 Chirality : 0.044 0.145 1381 Planarity : 0.004 0.055 1586 Dihedral : 5.141 52.064 1315 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 1.12 % Allowed : 11.66 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.26 (0.26), residues: 1128 helix: -0.83 (0.76), residues: 52 sheet: 0.36 (0.24), residues: 502 loop : -0.52 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 61 TYR 0.012 0.001 TYR E 91 PHE 0.018 0.001 PHE D 146 TRP 0.009 0.001 TRP F 50 HIS 0.003 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 9072) covalent geometry : angle 0.52364 / 0.27 (12348) SS BOND : bond 0.00225 / 0.13 ( 12) SS BOND : angle 0.76788 / 0.47 ( 24) hydrogen bonds : bond 0.02725 / 1.76 ( 333) hydrogen bonds : angle 5.23134 / 3.52 ( 897) link_BETA1-4 : bond 0.00105 / 0.06 ( 1) link_BETA1-4 : angle 1.62284 / 0.80 ( 3) link_BETA1-6 : bond 0.00450 / 0.24 ( 1) link_BETA1-6 : angle 1.42508 / 0.78 ( 3) link_NAG-ASN : bond 0.00200 / 0.10 ( 2) link_NAG-ASN : angle 1.34714 / 0.66 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 GLU cc_start: 0.6752 (pm20) cc_final: 0.5158 (pm20) REVERT: D 171 GLN cc_start: 0.7904 (mt0) cc_final: 0.7369 (mt0) REVERT: E 31 ASP cc_start: 0.8209 (t0) cc_final: 0.7833 (t0) REVERT: E 104 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: E 122 GLU cc_start: 0.9042 (mp0) cc_final: 0.8598 (mp0) REVERT: E 157 ASN cc_start: 0.9053 (m110) cc_final: 0.8490 (t0) REVERT: E 164 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: F 73 ASP cc_start: 0.8739 (t0) cc_final: 0.8394 (t0) REVERT: F 154 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7883 (tp30) REVERT: F 218 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7485 (tm-30) outliers start: 11 outliers final: 7 residues processed: 59 average time/residue: 0.8685 time to fit residues: 55.8109 Evaluate side-chains 59 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain G residue 199 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.104155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.072517 restraints weight = 56101.789| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.81 r_work: 0.3137 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1557 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1558 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9088 Z= 0.119 Angle : 0.521 7.539 12384 Z= 0.269 Chirality : 0.044 0.141 1381 Planarity : 0.004 0.055 1586 Dihedral : 5.046 52.290 1315 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.67 % Favored : 94.24 % Rotamer: Outliers : 1.22 % Allowed : 11.76 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.92 % 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: -0.23 (0.26), residues: 1128 helix: -0.80 (0.77), residues: 52 sheet: 0.38 (0.24), residues: 502 loop : -0.51 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 61 TYR 0.011 0.001 TYR E 91 PHE 0.015 0.001 PHE D 146 TRP 0.009 0.001 TRP D 50 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9072) covalent geometry : angle 0.51971 / 0.27 (12348) SS BOND : bond 0.00188 / 0.11 ( 12) SS BOND : angle 0.59432 / 0.37 ( 24) hydrogen bonds : bond 0.02674 / 1.73 ( 333) hydrogen bonds : angle 5.15092 / 3.47 ( 897) link_BETA1-4 : bond 0.00035 / 0.02 ( 1) link_BETA1-4 : angle 1.51564 / 0.74 ( 3) link_BETA1-6 : bond 0.00337 / 0.18 ( 1) link_BETA1-6 : angle 1.32971 / 0.73 ( 3) link_NAG-ASN : bond 0.00183 / 0.09 ( 2) link_NAG-ASN : angle 1.32988 / 0.65 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.04 seconds wall clock time: 86 minutes 43.66 seconds (5203.66 seconds total)