Starting phenix.real_space_refine on Tue Feb 3 22:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9y_19016/02_2026/8r9y_19016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9y_19016/02_2026/8r9y_19016.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 { model { file = "/net/cci-nas-00/data/ceres_data/8r9y_19016/02_2026/8r9y_19016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9y_19016/02_2026/8r9y_19016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r9y_19016/02_2026/8r9y_19016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9y_19016/02_2026/8r9y_19016.map" } 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= 0.013 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4685 2.51 5 N 1247 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7446 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1614 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain breaks: 1 Chain: "C" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 197} Chain: "H" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Time building chain proxies: 1.58, per 1000 atoms: 0.21 Number of scatterers: 7446 At special positions: 0 Unit cell: (73.9731, 107.066, 144.053, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1479 8.00 N 1247 7.00 C 4685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.05 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 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 D 1 " - " NAG D 2 " NAG-ASN " NAG A 501 " - " ASN A 331 " " NAG D 1 " - " ASN A 311 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 258.3 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 23 sheets defined 5.9% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 367 through 371 removed outlier: 4.024A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.721A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.701A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'H' and resid 195 through 198 removed outlier: 4.423A pdb=" N GLY H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 195 through 198' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.811A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.548A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.067A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 removed outlier: 8.650A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 11.673A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316 removed outlier: 6.690A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.680A pdb=" N VAL B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.318A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 57 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.812A pdb=" N ILE B 112 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.989A pdb=" N SER B 190 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER B 187 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 178 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 189 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.069A pdb=" N GLU C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.434A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.853A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.388A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.624A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 129 through 132 removed outlier: 3.617A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AC1, first strand: chain 'H' and resid 158 through 162 removed outlier: 4.191A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.708A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.676A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.506A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 145 through 150 removed outlier: 4.235A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2378 1.35 - 1.48: 2003 1.48 - 1.60: 3182 1.60 - 1.73: 0 1.73 - 1.86: 48 Bond restraints: 7611 Sorted by residual: bond pdb=" CB CYS A 335 " pdb=" SG CYS A 335 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 ... (remaining 7606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10257 2.49 - 4.99: 85 4.99 - 7.48: 10 7.48 - 9.98: 1 9.98 - 12.47: 1 Bond angle restraints: 10354 Sorted by residual: angle pdb=" CA CYS A 378 " pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " ideal model delta sigma weight residual 114.40 124.01 -9.61 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CA LEU B 200 " pdb=" CB LEU B 200 " pdb=" CG LEU B 200 " ideal model delta sigma weight residual 116.30 128.77 -12.47 3.50e+00 8.16e-02 1.27e+01 angle pdb=" C VAL L 150 " pdb=" N ASP L 151 " pdb=" CA ASP L 151 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.60e+00 angle pdb=" C PHE A 377 " pdb=" N CYS A 378 " pdb=" CA CYS A 378 " ideal model delta sigma weight residual 121.62 117.05 4.57 1.83e+00 2.99e-01 6.25e+00 angle pdb=" C LYS H 151 " pdb=" N ASP H 152 " pdb=" CA ASP H 152 " ideal model delta sigma weight residual 121.56 125.30 -3.74 1.56e+00 4.11e-01 5.75e+00 ... (remaining 10349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4169 17.32 - 34.63: 343 34.63 - 51.95: 64 51.95 - 69.27: 11 69.27 - 86.58: 12 Dihedral angle restraints: 4599 sinusoidal: 1793 harmonic: 2806 Sorted by residual: dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 206 " pdb=" CB CYS B 206 " ideal model delta sinusoidal sigma weight residual 93.00 141.01 -48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CB CYS A 335 " pdb=" SG CYS A 335 " pdb=" SG CYS A 378 " pdb=" CB CYS A 378 " ideal model delta sinusoidal sigma weight residual 93.00 46.38 46.62 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" N GLY B 107 " pdb=" CA GLY B 107 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 873 0.041 - 0.082: 198 0.082 - 0.123: 112 0.123 - 0.164: 7 0.164 - 0.205: 1 Chirality restraints: 1191 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE H 102 " pdb=" CA ILE H 102 " pdb=" CG1 ILE H 102 " pdb=" CG2 ILE H 102 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA PHE H 154 " pdb=" N PHE H 154 " pdb=" C PHE H 154 " pdb=" CB PHE H 154 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1188 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO L 80 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 394 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C TYR A 394 " -0.018 2.00e-02 2.50e+03 pdb=" O TYR A 394 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 395 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 43 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.10e+00 pdb=" N PRO L 44 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.015 5.00e-02 4.00e+02 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1584 2.78 - 3.31: 6436 3.31 - 3.84: 12037 3.84 - 4.37: 14202 4.37 - 4.90: 25621 Nonbonded interactions: 59880 Sorted by model distance: nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLN B 62 " pdb=" NH1 ARG B 65 " model vdw 2.266 3.120 nonbonded pdb=" O PRO H 131 " pdb=" OG SER L 121 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLU A 410 " pdb=" NH1 ARG H 99 " model vdw 2.311 3.120 nonbonded pdb=" O SER B 77 " pdb=" OG SER B 77 " model vdw 2.321 3.040 ... (remaining 59875 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 0.049 7625 Z= 0.142 Angle : 0.590 12.471 10385 Z= 0.298 Chirality : 0.044 0.205 1191 Planarity : 0.003 0.028 1315 Dihedral : 13.515 86.583 2766 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.13 (0.29), residues: 958 helix: -1.05 (0.90), residues: 31 sheet: 0.57 (0.25), residues: 470 loop : -0.25 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.011 0.001 TYR L 140 PHE 0.011 0.001 PHE H 154 TRP 0.007 0.001 TRP C 94 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7611) covalent geometry : angle 0.58576 (10354) SS BOND : bond 0.00574 ( 11) SS BOND : angle 1.42534 ( 22) hydrogen bonds : bond 0.25154 ( 269) hydrogen bonds : angle 10.67525 ( 714) link_BETA1-4 : bond 0.00121 ( 1) link_BETA1-4 : angle 1.75226 ( 3) link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.21495 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 THR cc_start: 0.8489 (m) cc_final: 0.8111 (p) REVERT: A 355 ASN cc_start: 0.8449 (m-40) cc_final: 0.8208 (p0) REVERT: A 412 GLN cc_start: 0.8701 (mm-40) cc_final: 0.7532 (tp-100) REVERT: B 29 PHE cc_start: 0.8573 (m-10) cc_final: 0.8193 (m-10) REVERT: B 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7860 (m-30) REVERT: C 18 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7669 (ttm-80) REVERT: C 24 TRP cc_start: 0.8019 (m-90) cc_final: 0.7755 (m100) REVERT: C 81 GLU cc_start: 0.8770 (pm20) cc_final: 0.8526 (pm20) REVERT: C 109 THR cc_start: 0.8739 (m) cc_final: 0.8525 (p) REVERT: C 143 GLU cc_start: 0.7495 (pp20) cc_final: 0.7196 (pp20) REVERT: C 167 ASP cc_start: 0.8172 (t70) cc_final: 0.7895 (t70) REVERT: C 199 GLN cc_start: 0.8795 (tt0) cc_final: 0.8280 (tm-30) REVERT: H 13 GLN cc_start: 0.8705 (mp10) cc_final: 0.8122 (mp10) REVERT: H 89 GLU cc_start: 0.8320 (pm20) cc_final: 0.7901 (pm20) REVERT: L 158 ASN cc_start: 0.8195 (t0) cc_final: 0.7873 (p0) REVERT: L 161 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7842 (mt-10) REVERT: L 167 ASP cc_start: 0.8405 (t0) cc_final: 0.7813 (t70) REVERT: L 185 ASP cc_start: 0.8945 (m-30) cc_final: 0.8619 (t70) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5799 time to fit residues: 95.0292 Evaluate side-chains 85 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 63 ASN C 124 GLN C 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069662 restraints weight = 16871.907| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.16 r_work: 0.2961 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7625 Z= 0.162 Angle : 0.644 9.470 10385 Z= 0.335 Chirality : 0.046 0.143 1191 Planarity : 0.004 0.033 1315 Dihedral : 5.332 53.411 1105 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.79 % Allowed : 11.60 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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 (0.29), residues: 958 helix: -0.91 (0.85), residues: 31 sheet: 0.65 (0.25), residues: 470 loop : -0.22 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 54 TYR 0.009 0.001 TYR L 140 PHE 0.012 0.001 PHE H 154 TRP 0.007 0.001 TRP H 36 HIS 0.007 0.001 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7611) covalent geometry : angle 0.64043 (10354) SS BOND : bond 0.00612 ( 11) SS BOND : angle 1.48831 ( 22) hydrogen bonds : bond 0.04090 ( 269) hydrogen bonds : angle 7.38909 ( 714) link_BETA1-4 : bond 0.00168 ( 1) link_BETA1-4 : angle 1.44550 ( 3) link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 0.96921 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 THR cc_start: 0.8616 (m) cc_final: 0.8369 (p) REVERT: A 355 ASN cc_start: 0.8572 (m-40) cc_final: 0.8303 (p0) REVERT: A 412 GLN cc_start: 0.8795 (mm-40) cc_final: 0.7660 (tp-100) REVERT: B 73 ASP cc_start: 0.8120 (t0) cc_final: 0.7465 (t70) REVERT: B 205 ILE cc_start: 0.7959 (tt) cc_final: 0.7672 (tp) REVERT: B 222 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: C 18 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7668 (ttm-80) REVERT: C 109 THR cc_start: 0.8700 (m) cc_final: 0.8486 (p) REVERT: C 199 GLN cc_start: 0.8822 (tt0) cc_final: 0.8253 (tm-30) REVERT: H 13 GLN cc_start: 0.8832 (mp10) cc_final: 0.8138 (mp10) REVERT: H 89 GLU cc_start: 0.8573 (pm20) cc_final: 0.8240 (pm20) REVERT: H 103 MET cc_start: 0.7720 (mtp) cc_final: 0.7395 (mtp) REVERT: L 122 ASP cc_start: 0.8647 (p0) cc_final: 0.8013 (p0) REVERT: L 123 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7261 (mp0) REVERT: L 145 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8487 (tptp) REVERT: L 147 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: L 154 LEU cc_start: 0.8241 (mm) cc_final: 0.7984 (tt) REVERT: L 158 ASN cc_start: 0.8254 (t0) cc_final: 0.7990 (p0) REVERT: L 167 ASP cc_start: 0.8443 (t0) cc_final: 0.7872 (t70) REVERT: L 185 ASP cc_start: 0.8949 (m-30) cc_final: 0.8616 (t70) outliers start: 15 outliers final: 7 residues processed: 103 average time/residue: 0.4574 time to fit residues: 49.7978 Evaluate side-chains 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072801 restraints weight = 17039.969| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.10 r_work: 0.3060 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7625 Z= 0.117 Angle : 0.589 8.464 10385 Z= 0.302 Chirality : 0.045 0.193 1191 Planarity : 0.003 0.032 1315 Dihedral : 5.155 53.245 1105 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.63 % Allowed : 13.40 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.28 (0.29), residues: 958 helix: -0.49 (0.92), residues: 29 sheet: 0.60 (0.24), residues: 480 loop : -0.12 (0.33), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.010 0.001 TYR H 95 PHE 0.009 0.001 PHE A 374 TRP 0.008 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7611) covalent geometry : angle 0.58608 (10354) SS BOND : bond 0.00605 ( 11) SS BOND : angle 1.24141 ( 22) hydrogen bonds : bond 0.03227 ( 269) hydrogen bonds : angle 6.47852 ( 714) link_BETA1-4 : bond 0.00126 ( 1) link_BETA1-4 : angle 1.44488 ( 3) link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 0.98055 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8780 (mm-40) cc_final: 0.7728 (tp-100) REVERT: B 73 ASP cc_start: 0.8246 (t0) cc_final: 0.7658 (t70) REVERT: B 222 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: C 18 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7662 (ttm-80) REVERT: C 54 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.8026 (ttm170) REVERT: C 124 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: C 199 GLN cc_start: 0.8734 (tt0) cc_final: 0.8427 (tm-30) REVERT: H 13 GLN cc_start: 0.8886 (mp10) cc_final: 0.8219 (mp10) REVERT: H 89 GLU cc_start: 0.8471 (pm20) cc_final: 0.8196 (pm20) REVERT: H 103 MET cc_start: 0.7946 (mtp) cc_final: 0.7562 (mtp) REVERT: L 122 ASP cc_start: 0.8525 (p0) cc_final: 0.7806 (p0) REVERT: L 123 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7361 (mp0) REVERT: L 145 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8633 (tptp) REVERT: L 147 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: L 167 ASP cc_start: 0.8434 (t0) cc_final: 0.7911 (t70) REVERT: L 185 ASP cc_start: 0.8934 (m-30) cc_final: 0.8674 (t70) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 0.4370 time to fit residues: 52.8358 Evaluate side-chains 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 63 ASN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071614 restraints weight = 17001.939| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.30 r_work: 0.2991 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7625 Z= 0.108 Angle : 0.578 8.137 10385 Z= 0.297 Chirality : 0.045 0.158 1191 Planarity : 0.003 0.031 1315 Dihedral : 5.051 53.111 1105 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.75 % Allowed : 15.07 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.37 (0.29), residues: 958 helix: -0.63 (0.96), residues: 29 sheet: 0.70 (0.24), residues: 479 loop : -0.09 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 54 TYR 0.010 0.001 TYR H 95 PHE 0.009 0.001 PHE A 374 TRP 0.008 0.001 TRP B 164 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7611) covalent geometry : angle 0.57569 (10354) SS BOND : bond 0.00596 ( 11) SS BOND : angle 1.19223 ( 22) hydrogen bonds : bond 0.02931 ( 269) hydrogen bonds : angle 6.09143 ( 714) link_BETA1-4 : bond 0.00163 ( 1) link_BETA1-4 : angle 1.40196 ( 3) link_NAG-ASN : bond 0.00130 ( 2) link_NAG-ASN : angle 0.88384 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8808 (mm-40) cc_final: 0.7729 (tp-100) REVERT: B 73 ASP cc_start: 0.8162 (t0) cc_final: 0.7479 (t70) REVERT: B 222 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: C 18 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7607 (ttm-80) REVERT: C 54 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8013 (ttm170) REVERT: C 185 ASP cc_start: 0.6635 (p0) cc_final: 0.6155 (t0) REVERT: C 199 GLN cc_start: 0.8794 (tt0) cc_final: 0.8427 (tm-30) REVERT: H 13 GLN cc_start: 0.8814 (mp10) cc_final: 0.8118 (mp10) REVERT: H 65 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8616 (tptm) REVERT: H 89 GLU cc_start: 0.8509 (pm20) cc_final: 0.8194 (pm20) REVERT: H 103 MET cc_start: 0.7779 (mtp) cc_final: 0.7388 (mtp) REVERT: L 31 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.7897 (t0) REVERT: L 122 ASP cc_start: 0.8625 (p0) cc_final: 0.7999 (p0) REVERT: L 123 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7403 (mp0) REVERT: L 145 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8590 (tptp) REVERT: L 147 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: L 167 ASP cc_start: 0.8497 (t0) cc_final: 0.7889 (t70) REVERT: L 185 ASP cc_start: 0.8948 (m-30) cc_final: 0.8666 (t70) outliers start: 23 outliers final: 12 residues processed: 117 average time/residue: 0.4705 time to fit residues: 58.0786 Evaluate side-chains 98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 124 GLN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.076533 restraints weight = 17411.574| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.90 r_work: 0.3131 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7625 Z= 0.151 Angle : 0.599 8.181 10385 Z= 0.307 Chirality : 0.045 0.153 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.124 52.708 1105 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.47 % Allowed : 15.79 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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 (0.29), residues: 958 helix: -0.68 (0.97), residues: 29 sheet: 0.67 (0.24), residues: 470 loop : -0.13 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.009 0.001 TYR H 95 PHE 0.011 0.001 PHE H 154 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7611) covalent geometry : angle 0.59512 (10354) SS BOND : bond 0.00667 ( 11) SS BOND : angle 1.39695 ( 22) hydrogen bonds : bond 0.02975 ( 269) hydrogen bonds : angle 5.99756 ( 714) link_BETA1-4 : bond 0.00002 ( 1) link_BETA1-4 : angle 1.50530 ( 3) link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 0.93820 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8714 (mm-40) cc_final: 0.7711 (tp-100) REVERT: B 73 ASP cc_start: 0.8313 (t0) cc_final: 0.7713 (t70) REVERT: B 111 ASP cc_start: 0.9018 (p0) cc_final: 0.8772 (p0) REVERT: B 222 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: C 18 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7691 (ttm-80) REVERT: C 199 GLN cc_start: 0.8754 (tt0) cc_final: 0.8456 (tm-30) REVERT: H 13 GLN cc_start: 0.8865 (mp10) cc_final: 0.8192 (mp10) REVERT: H 89 GLU cc_start: 0.8440 (pm20) cc_final: 0.8179 (pm20) REVERT: H 103 MET cc_start: 0.8066 (mtp) cc_final: 0.7680 (mtp) REVERT: L 31 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8097 (t0) REVERT: L 122 ASP cc_start: 0.8552 (p0) cc_final: 0.7836 (p0) REVERT: L 123 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7479 (mp0) REVERT: L 125 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7272 (mm) REVERT: L 145 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8627 (tptp) REVERT: L 147 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: L 167 ASP cc_start: 0.8488 (t0) cc_final: 0.7990 (t70) REVERT: L 185 ASP cc_start: 0.8956 (m-30) cc_final: 0.8751 (t70) outliers start: 29 outliers final: 13 residues processed: 107 average time/residue: 0.4002 time to fit residues: 45.4717 Evaluate side-chains 97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075101 restraints weight = 17305.723| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.87 r_work: 0.3097 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7625 Z= 0.198 Angle : 0.638 8.651 10385 Z= 0.327 Chirality : 0.046 0.155 1191 Planarity : 0.003 0.026 1315 Dihedral : 5.252 52.579 1105 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.87 % Allowed : 17.82 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.21 (0.29), residues: 958 helix: -0.84 (0.95), residues: 29 sheet: 0.60 (0.24), residues: 470 loop : -0.20 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.011 0.001 TYR L 140 PHE 0.015 0.001 PHE H 154 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7611) covalent geometry : angle 0.63372 (10354) SS BOND : bond 0.00652 ( 11) SS BOND : angle 1.50274 ( 22) hydrogen bonds : bond 0.03094 ( 269) hydrogen bonds : angle 6.03072 ( 714) link_BETA1-4 : bond 0.00067 ( 1) link_BETA1-4 : angle 1.62642 ( 3) link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 1.10512 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8717 (mm-40) cc_final: 0.7689 (tp-100) REVERT: B 73 ASP cc_start: 0.8337 (t0) cc_final: 0.7689 (t70) REVERT: B 111 ASP cc_start: 0.9034 (p0) cc_final: 0.8816 (p0) REVERT: B 222 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: C 199 GLN cc_start: 0.8748 (tt0) cc_final: 0.8475 (tm-30) REVERT: H 13 GLN cc_start: 0.8874 (mp10) cc_final: 0.8205 (mp10) REVERT: H 89 GLU cc_start: 0.8451 (pm20) cc_final: 0.8195 (pm20) REVERT: H 103 MET cc_start: 0.8113 (mtp) cc_final: 0.7728 (mtp) REVERT: L 31 ASN cc_start: 0.8557 (t0) cc_final: 0.8124 (t0) REVERT: L 122 ASP cc_start: 0.8553 (p0) cc_final: 0.7926 (p0) REVERT: L 123 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7467 (mp0) REVERT: L 125 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7281 (mm) REVERT: L 142 ARG cc_start: 0.7475 (ttt90) cc_final: 0.7243 (tpt-90) REVERT: L 145 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8646 (tptp) REVERT: L 147 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: L 167 ASP cc_start: 0.8500 (t0) cc_final: 0.7991 (t70) outliers start: 24 outliers final: 15 residues processed: 102 average time/residue: 0.4834 time to fit residues: 52.2582 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 124 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074375 restraints weight = 17228.478| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.98 r_work: 0.3120 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7625 Z= 0.156 Angle : 0.607 8.236 10385 Z= 0.313 Chirality : 0.045 0.149 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.217 53.083 1105 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.23 % Allowed : 18.30 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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 (0.29), residues: 958 helix: -0.89 (0.95), residues: 29 sheet: 0.62 (0.24), residues: 467 loop : -0.18 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.011 0.001 TYR L 140 PHE 0.013 0.001 PHE H 154 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7611) covalent geometry : angle 0.60383 (10354) SS BOND : bond 0.00621 ( 11) SS BOND : angle 1.38310 ( 22) hydrogen bonds : bond 0.02917 ( 269) hydrogen bonds : angle 5.89506 ( 714) link_BETA1-4 : bond 0.00045 ( 1) link_BETA1-4 : angle 1.57252 ( 3) link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 1.12185 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8702 (mm-40) cc_final: 0.7692 (tp-100) REVERT: B 73 ASP cc_start: 0.8331 (t0) cc_final: 0.7696 (t70) REVERT: B 111 ASP cc_start: 0.9012 (p0) cc_final: 0.8799 (p0) REVERT: B 222 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7449 (pp20) REVERT: C 199 GLN cc_start: 0.8743 (tt0) cc_final: 0.8495 (tm-30) REVERT: H 13 GLN cc_start: 0.8925 (mp10) cc_final: 0.8277 (mp10) REVERT: H 87 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7143 (mtm-85) REVERT: H 89 GLU cc_start: 0.8393 (pm20) cc_final: 0.8167 (pm20) REVERT: H 103 MET cc_start: 0.8149 (mtp) cc_final: 0.7750 (mtp) REVERT: L 31 ASN cc_start: 0.8387 (t0) cc_final: 0.7999 (t0) REVERT: L 122 ASP cc_start: 0.8504 (p0) cc_final: 0.7976 (p0) REVERT: L 123 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7452 (mp0) REVERT: L 125 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7310 (mm) REVERT: L 142 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7297 (tpt-90) REVERT: L 147 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: L 167 ASP cc_start: 0.8503 (t0) cc_final: 0.8009 (t70) outliers start: 27 outliers final: 14 residues processed: 104 average time/residue: 0.4703 time to fit residues: 51.9367 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068650 restraints weight = 17744.081| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.13 r_work: 0.2986 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7625 Z= 0.275 Angle : 0.707 10.745 10385 Z= 0.363 Chirality : 0.048 0.166 1191 Planarity : 0.004 0.028 1315 Dihedral : 5.535 52.346 1105 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.99 % Allowed : 19.74 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.01 (0.28), residues: 958 helix: -1.46 (0.86), residues: 31 sheet: 0.45 (0.24), residues: 471 loop : -0.26 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.013 0.002 TYR L 140 PHE 0.018 0.002 PHE H 154 TRP 0.010 0.002 TRP H 47 HIS 0.005 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 7611) covalent geometry : angle 0.70139 (10354) SS BOND : bond 0.00795 ( 11) SS BOND : angle 1.84920 ( 22) hydrogen bonds : bond 0.03383 ( 269) hydrogen bonds : angle 6.25062 ( 714) link_BETA1-4 : bond 0.00301 ( 1) link_BETA1-4 : angle 1.91182 ( 3) link_NAG-ASN : bond 0.00165 ( 2) link_NAG-ASN : angle 1.37728 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 333 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8612 (m) REVERT: A 412 GLN cc_start: 0.8750 (mm-40) cc_final: 0.7681 (tp-100) REVERT: B 73 ASP cc_start: 0.8291 (t0) cc_final: 0.7611 (t70) REVERT: B 222 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: C 199 GLN cc_start: 0.8777 (tt0) cc_final: 0.8505 (tm-30) REVERT: H 13 GLN cc_start: 0.8932 (mp10) cc_final: 0.8289 (mp10) REVERT: H 89 GLU cc_start: 0.8486 (pm20) cc_final: 0.8253 (pm20) REVERT: L 31 ASN cc_start: 0.8593 (t0) cc_final: 0.8078 (t0) REVERT: L 122 ASP cc_start: 0.8684 (p0) cc_final: 0.8111 (p0) REVERT: L 123 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7540 (mp0) REVERT: L 125 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7191 (mm) REVERT: L 142 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7253 (tpt-90) REVERT: L 167 ASP cc_start: 0.8575 (t0) cc_final: 0.8045 (t70) outliers start: 25 outliers final: 17 residues processed: 96 average time/residue: 0.4816 time to fit residues: 48.9344 Evaluate side-chains 93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071296 restraints weight = 17171.221| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.11 r_work: 0.3023 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7625 Z= 0.140 Angle : 0.618 9.510 10385 Z= 0.318 Chirality : 0.045 0.145 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.331 53.685 1105 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.51 % Allowed : 20.33 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.14 (0.29), residues: 958 helix: -1.03 (0.92), residues: 29 sheet: 0.53 (0.24), residues: 467 loop : -0.19 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.012 0.001 TYR L 140 PHE 0.013 0.001 PHE H 154 TRP 0.008 0.001 TRP B 164 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7611) covalent geometry : angle 0.61321 (10354) SS BOND : bond 0.00697 ( 11) SS BOND : angle 1.55977 ( 22) hydrogen bonds : bond 0.02790 ( 269) hydrogen bonds : angle 5.88322 ( 714) link_BETA1-4 : bond 0.00095 ( 1) link_BETA1-4 : angle 1.63457 ( 3) link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 1.22950 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8733 (mm-40) cc_final: 0.7658 (tp-100) REVERT: B 73 ASP cc_start: 0.8263 (t0) cc_final: 0.7577 (t70) REVERT: B 222 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: C 199 GLN cc_start: 0.8730 (tt0) cc_final: 0.8496 (tm-30) REVERT: H 13 GLN cc_start: 0.8930 (mp10) cc_final: 0.8278 (mp10) REVERT: H 87 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: H 89 GLU cc_start: 0.8419 (pm20) cc_final: 0.8195 (pm20) REVERT: H 103 MET cc_start: 0.8088 (mtp) cc_final: 0.7764 (mtp) REVERT: L 31 ASN cc_start: 0.8448 (t0) cc_final: 0.7967 (t0) REVERT: L 122 ASP cc_start: 0.8605 (p0) cc_final: 0.8028 (p0) REVERT: L 123 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7449 (mp0) REVERT: L 125 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7297 (mm) REVERT: L 142 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7167 (tpt-90) REVERT: L 167 ASP cc_start: 0.8531 (t0) cc_final: 0.7988 (t70) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.5422 time to fit residues: 52.8483 Evaluate side-chains 90 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071882 restraints weight = 17151.654| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.12 r_work: 0.3032 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7625 Z= 0.133 Angle : 0.614 9.187 10385 Z= 0.313 Chirality : 0.045 0.141 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.218 53.378 1105 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.51 % Allowed : 20.33 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.19 (0.29), residues: 958 helix: -0.93 (0.93), residues: 29 sheet: 0.58 (0.24), residues: 468 loop : -0.18 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.012 0.001 TYR L 140 PHE 0.009 0.001 PHE A 374 TRP 0.007 0.001 TRP C 94 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7611) covalent geometry : angle 0.61028 (10354) SS BOND : bond 0.00657 ( 11) SS BOND : angle 1.46469 ( 22) hydrogen bonds : bond 0.02724 ( 269) hydrogen bonds : angle 5.74446 ( 714) link_BETA1-4 : bond 0.00051 ( 1) link_BETA1-4 : angle 1.57486 ( 3) link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 1.16501 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 333 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8466 (m) REVERT: A 412 GLN cc_start: 0.8720 (mm-40) cc_final: 0.7653 (tp-100) REVERT: B 73 ASP cc_start: 0.8267 (t0) cc_final: 0.7564 (t70) REVERT: C 154 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8270 (tm) REVERT: C 199 GLN cc_start: 0.8695 (tt0) cc_final: 0.8476 (tm-30) REVERT: H 13 GLN cc_start: 0.8894 (mp10) cc_final: 0.8217 (mp10) REVERT: H 87 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7133 (mtm-85) REVERT: L 31 ASN cc_start: 0.8401 (t0) cc_final: 0.7978 (t0) REVERT: L 122 ASP cc_start: 0.8601 (p0) cc_final: 0.7958 (p0) REVERT: L 123 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7481 (mp0) REVERT: L 125 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7271 (mm) REVERT: L 142 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7155 (tpt-90) REVERT: L 167 ASP cc_start: 0.8516 (t0) cc_final: 0.7979 (t70) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 0.5212 time to fit residues: 51.4683 Evaluate side-chains 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072076 restraints weight = 16989.803| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.09 r_work: 0.3047 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7625 Z= 0.135 Angle : 0.604 8.907 10385 Z= 0.311 Chirality : 0.045 0.139 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.201 53.375 1105 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.75 % Allowed : 19.98 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 0.21 (0.29), residues: 958 helix: -0.91 (0.93), residues: 29 sheet: 0.61 (0.24), residues: 468 loop : -0.20 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 142 TYR 0.012 0.001 TYR L 140 PHE 0.011 0.001 PHE H 154 TRP 0.007 0.001 TRP B 113 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7611) covalent geometry : angle 0.59970 (10354) SS BOND : bond 0.00650 ( 11) SS BOND : angle 1.45662 ( 22) hydrogen bonds : bond 0.02704 ( 269) hydrogen bonds : angle 5.68685 ( 714) link_BETA1-4 : bond 0.00094 ( 1) link_BETA1-4 : angle 1.54253 ( 3) link_NAG-ASN : bond 0.00056 ( 2) link_NAG-ASN : angle 1.10821 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.26 seconds wall clock time: 33 minutes 49.27 seconds (2029.27 seconds total)