Starting phenix.real_space_refine on Fri Oct 10 16:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9z_19017/10_2025/8r9z_19017.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9z_19017/10_2025/8r9z_19017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r9z_19017/10_2025/8r9z_19017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9z_19017/10_2025/8r9z_19017.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9z_19017/10_2025/8r9z_19017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9z_19017/10_2025/8r9z_19017.cif" } resolution = 2.9 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= 0.012 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 4682 2.51 5 N 1246 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7441 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: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1654 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: 1.86, per 1000 atoms: 0.25 Number of scatterers: 7441 At special positions: 0 Unit cell: (73.9731, 105.12, 145.026, 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 1478 8.00 N 1246 7.00 C 4682 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: 0.63 Conformation dependent library (CDL) restraints added in 401.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 24 sheets defined 6.4% alpha, 49.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.801A pdb=" N ASN A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.707A 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 188 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.700A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.634A 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: 4.319A 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: 3.687A 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: 3.523A 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: 6.154A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.926A 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: 8.393A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 11.233A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 11.798A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.484A 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: 6.870A 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 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.581A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.641A 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 134 removed outlier: 3.549A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 190 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 134 removed outlier: 3.549A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 190 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.119A pdb=" N GLU C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.631A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.849A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.355A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.649A pdb=" N CYS C 194 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.653A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.640A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB9, first strand: chain 'H' and resid 129 through 131 removed outlier: 5.781A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AC2, first strand: chain 'H' and resid 158 through 162 removed outlier: 4.604A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.832A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.657A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.705A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 145 through 150 removed outlier: 4.309A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR L 197 " --> pdb=" O LYS L 145 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 762 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: 1.36 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2374 1.35 - 1.47: 2001 1.47 - 1.60: 3183 1.60 - 1.72: 0 1.72 - 1.85: 48 Bond restraints: 7606 Sorted by residual: 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 1.62e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" CB CYS A 335 " pdb=" SG CYS A 335 " ideal model delta sigma weight residual 1.808 1.850 -0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+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 1.22e+00 ... (remaining 7601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 10246 2.40 - 4.80: 87 4.80 - 7.21: 12 7.21 - 9.61: 1 9.61 - 12.01: 1 Bond angle restraints: 10347 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 114.40 122.57 -8.17 2.30e+00 1.89e-01 1.26e+01 angle pdb=" CA LEU B 200 " pdb=" CB LEU B 200 " pdb=" CG LEU B 200 " ideal model delta sigma weight residual 116.30 128.31 -12.01 3.50e+00 8.16e-02 1.18e+01 angle pdb=" N VAL L 150 " pdb=" CA VAL L 150 " pdb=" C VAL L 150 " ideal model delta sigma weight residual 106.21 109.65 -3.44 1.07e+00 8.73e-01 1.03e+01 angle pdb=" C VAL L 150 " pdb=" N ASP L 151 " pdb=" CA ASP L 151 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C LYS H 151 " pdb=" N ASP H 152 " pdb=" CA ASP H 152 " ideal model delta sigma weight residual 121.26 125.93 -4.67 1.59e+00 3.96e-01 8.64e+00 ... (remaining 10342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4181 16.79 - 33.58: 322 33.58 - 50.36: 63 50.36 - 67.15: 18 67.15 - 83.94: 11 Dihedral angle restraints: 4595 sinusoidal: 1790 harmonic: 2805 Sorted by residual: dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 153.27 -60.27 1 1.00e+01 1.00e-02 4.84e+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 47.21 45.79 1 1.00e+01 1.00e-02 2.91e+01 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 93.00 138.25 -45.25 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 4592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 852 0.040 - 0.080: 211 0.080 - 0.120: 115 0.120 - 0.160: 12 0.160 - 0.200: 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 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 52 " pdb=" N ILE B 52 " pdb=" C ILE B 52 " pdb=" CB ILE B 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1188 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 194 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 195 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO L 80 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 166 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C GLN C 166 " -0.021 2.00e-02 2.50e+03 pdb=" O GLN C 166 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP C 167 " 0.007 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1929 2.80 - 3.33: 6285 3.33 - 3.85: 11995 3.85 - 4.38: 14282 4.38 - 4.90: 25642 Nonbonded interactions: 60133 Sorted by model distance: nonbonded pdb=" OG SER C 121 " pdb=" OE1 GLU C 123 " model vdw 2.276 3.040 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.277 3.040 nonbonded pdb=" O ASP C 82 " pdb=" OH TYR C 86 " model vdw 2.300 3.040 nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLN B 62 " pdb=" NH1 ARG B 65 " model vdw 2.310 3.120 ... (remaining 60128 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: 1.730 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.730 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 0.042 7620 Z= 0.132 Angle : 0.571 12.009 10378 Z= 0.291 Chirality : 0.044 0.200 1191 Planarity : 0.004 0.044 1314 Dihedral : 13.351 83.940 2762 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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 aren not related in a simple way. whole: 0.16 (0.29), residues: 958 helix: -1.80 (0.81), residues: 30 sheet: 0.45 (0.25), residues: 463 loop : 0.00 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 105 TYR 0.012 0.001 TYR L 140 PHE 0.008 0.001 PHE L 71 TRP 0.008 0.001 TRP C 94 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7606) covalent geometry : angle 0.56764 (10347) SS BOND : bond 0.00522 ( 11) SS BOND : angle 1.27788 ( 22) hydrogen bonds : bond 0.23814 ( 277) hydrogen bonds : angle 10.84969 ( 762) link_BETA1-4 : bond 0.00092 ( 1) link_BETA1-4 : angle 1.68492 ( 3) link_NAG-ASN : bond 0.00162 ( 2) link_NAG-ASN : angle 0.69160 ( 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 126 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ASN cc_start: 0.8692 (m-40) cc_final: 0.8467 (p0) REVERT: B 43 GLN cc_start: 0.8994 (mm110) cc_final: 0.8781 (mm110) REVERT: H 12 VAL cc_start: 0.9025 (p) cc_final: 0.8761 (m) REVERT: H 89 GLU cc_start: 0.8450 (pm20) cc_final: 0.8175 (pm20) REVERT: L 17 ASP cc_start: 0.8309 (m-30) cc_final: 0.8089 (m-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.7099 time to fit residues: 93.4679 Evaluate side-chains 88 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068665 restraints weight = 18129.538| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.91 r_work: 0.3021 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7620 Z= 0.202 Angle : 0.665 9.408 10378 Z= 0.348 Chirality : 0.047 0.178 1191 Planarity : 0.004 0.034 1314 Dihedral : 5.322 51.187 1104 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.44 % Allowed : 9.58 % Favored : 88.98 % 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 aren not related in a simple way. whole: 0.26 (0.29), residues: 958 helix: -1.68 (0.86), residues: 31 sheet: 0.57 (0.24), residues: 467 loop : 0.02 (0.33), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 142 TYR 0.013 0.001 TYR L 140 PHE 0.012 0.001 PHE B 156 TRP 0.008 0.001 TRP C 94 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 7606) covalent geometry : angle 0.66134 (10347) SS BOND : bond 0.00629 ( 11) SS BOND : angle 1.63050 ( 22) hydrogen bonds : bond 0.04606 ( 277) hydrogen bonds : angle 7.13117 ( 762) link_BETA1-4 : bond 0.00105 ( 1) link_BETA1-4 : angle 1.34990 ( 3) link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 0.71920 ( 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 99 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 333 SER cc_start: 0.9022 (t) cc_final: 0.8787 (p) REVERT: B 43 GLN cc_start: 0.9154 (mm110) cc_final: 0.8875 (mm110) REVERT: B 222 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: C 18 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8210 (ttm110) REVERT: C 123 GLU cc_start: 0.7852 (mp0) cc_final: 0.7646 (mp0) REVERT: H 89 GLU cc_start: 0.8820 (pm20) cc_final: 0.8395 (pm20) REVERT: L 4 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.8987 (mmm) REVERT: L 17 ASP cc_start: 0.8303 (m-30) cc_final: 0.8029 (m-30) REVERT: L 24 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8083 (mtp-110) REVERT: L 142 ARG cc_start: 0.8438 (ttt-90) cc_final: 0.8100 (tmt90) REVERT: L 145 LYS cc_start: 0.8169 (pttt) cc_final: 0.7929 (ptmm) outliers start: 12 outliers final: 4 residues processed: 91 average time/residue: 0.7426 time to fit residues: 70.6382 Evaluate side-chains 84 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 123 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 370 ASN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067939 restraints weight = 17774.446| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.93 r_work: 0.2985 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7620 Z= 0.157 Angle : 0.616 8.157 10378 Z= 0.323 Chirality : 0.045 0.180 1191 Planarity : 0.004 0.034 1314 Dihedral : 5.238 51.204 1104 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.56 % Allowed : 12.57 % Favored : 85.87 % 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 aren not related in a simple way. whole: 0.31 (0.29), residues: 958 helix: -1.41 (0.90), residues: 31 sheet: 0.58 (0.24), residues: 466 loop : 0.06 (0.33), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 54 TYR 0.012 0.001 TYR L 140 PHE 0.011 0.001 PHE H 154 TRP 0.008 0.001 TRP C 94 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7606) covalent geometry : angle 0.61313 (10347) SS BOND : bond 0.00577 ( 11) SS BOND : angle 1.42424 ( 22) hydrogen bonds : bond 0.03662 ( 277) hydrogen bonds : angle 6.34656 ( 762) link_BETA1-4 : bond 0.00206 ( 1) link_BETA1-4 : angle 1.41788 ( 3) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 0.75386 ( 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 100 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 334 TYR cc_start: 0.8450 (t80) cc_final: 0.8145 (t80) REVERT: B 43 GLN cc_start: 0.9191 (mm110) cc_final: 0.8890 (mm110) REVERT: B 207 ASN cc_start: 0.8507 (m-40) cc_final: 0.8284 (m-40) REVERT: B 222 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: C 18 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8265 (ttm110) REVERT: C 123 GLU cc_start: 0.7844 (mp0) cc_final: 0.7570 (mp0) REVERT: H 89 GLU cc_start: 0.8835 (pm20) cc_final: 0.8363 (pm20) REVERT: L 4 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8910 (mmm) REVERT: L 17 ASP cc_start: 0.8312 (m-30) cc_final: 0.8022 (m-30) REVERT: L 142 ARG cc_start: 0.8509 (ttt-90) cc_final: 0.8234 (tmt90) REVERT: L 145 LYS cc_start: 0.8141 (pttt) cc_final: 0.7928 (ptmm) REVERT: L 187 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8323 (mm-30) outliers start: 13 outliers final: 4 residues processed: 94 average time/residue: 0.6820 time to fit residues: 67.4380 Evaluate side-chains 87 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.083804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069367 restraints weight = 18005.677| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.01 r_work: 0.3007 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7620 Z= 0.116 Angle : 0.587 7.473 10378 Z= 0.305 Chirality : 0.044 0.178 1191 Planarity : 0.004 0.031 1314 Dihedral : 5.114 51.808 1104 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.04 % Allowed : 13.65 % Favored : 84.31 % 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 aren not related in a simple way. whole: 0.35 (0.29), residues: 958 helix: -1.44 (0.88), residues: 31 sheet: 0.63 (0.24), residues: 458 loop : 0.07 (0.32), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 24 TYR 0.012 0.001 TYR L 140 PHE 0.009 0.001 PHE H 154 TRP 0.008 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7606) covalent geometry : angle 0.58336 (10347) SS BOND : bond 0.00574 ( 11) SS BOND : angle 1.38137 ( 22) hydrogen bonds : bond 0.03033 ( 277) hydrogen bonds : angle 5.84702 ( 762) link_BETA1-4 : bond 0.00235 ( 1) link_BETA1-4 : angle 1.33972 ( 3) link_NAG-ASN : bond 0.00214 ( 2) link_NAG-ASN : angle 0.76667 ( 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 103 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 334 TYR cc_start: 0.8422 (t80) cc_final: 0.8146 (t80) REVERT: B 43 GLN cc_start: 0.9178 (mm110) cc_final: 0.8870 (mm110) REVERT: B 207 ASN cc_start: 0.8440 (m-40) cc_final: 0.8223 (m-40) REVERT: B 222 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: C 123 GLU cc_start: 0.7854 (mp0) cc_final: 0.7533 (mp0) REVERT: H 89 GLU cc_start: 0.8837 (pm20) cc_final: 0.8338 (pm20) REVERT: L 4 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8838 (mmm) REVERT: L 17 ASP cc_start: 0.8339 (m-30) cc_final: 0.8028 (m-30) REVERT: L 18 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.8535 (ttt-90) REVERT: L 24 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8064 (mtp-110) REVERT: L 142 ARG cc_start: 0.8516 (ttt-90) cc_final: 0.8267 (tmt90) REVERT: L 165 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: L 187 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8324 (mm-30) outliers start: 17 outliers final: 3 residues processed: 95 average time/residue: 0.7604 time to fit residues: 75.5688 Evaluate side-chains 84 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.082166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068231 restraints weight = 17932.280| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.90 r_work: 0.2995 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7620 Z= 0.153 Angle : 0.602 7.572 10378 Z= 0.313 Chirality : 0.045 0.182 1191 Planarity : 0.004 0.031 1314 Dihedral : 5.119 51.163 1104 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.68 % Allowed : 14.97 % Favored : 83.35 % 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 aren not related in a simple way. whole: 0.35 (0.28), residues: 958 helix: -1.43 (0.88), residues: 31 sheet: 0.61 (0.24), residues: 464 loop : 0.07 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 54 TYR 0.012 0.001 TYR L 140 PHE 0.010 0.001 PHE H 154 TRP 0.007 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7606) covalent geometry : angle 0.59895 (10347) SS BOND : bond 0.00606 ( 11) SS BOND : angle 1.41563 ( 22) hydrogen bonds : bond 0.03003 ( 277) hydrogen bonds : angle 5.68734 ( 762) link_BETA1-4 : bond 0.00072 ( 1) link_BETA1-4 : angle 1.40872 ( 3) link_NAG-ASN : bond 0.00144 ( 2) link_NAG-ASN : angle 0.72743 ( 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 97 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9194 (mm110) cc_final: 0.8895 (mm110) REVERT: H 89 GLU cc_start: 0.8826 (pm20) cc_final: 0.8434 (pm20) REVERT: L 4 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8874 (mmm) REVERT: L 17 ASP cc_start: 0.8331 (m-30) cc_final: 0.8030 (m-30) REVERT: L 24 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8087 (mtp-110) REVERT: L 81 GLU cc_start: 0.8976 (mp0) cc_final: 0.8721 (pm20) REVERT: L 142 ARG cc_start: 0.8530 (ttt-90) cc_final: 0.8315 (tmt90) REVERT: L 165 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: L 187 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8345 (mm-30) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.7299 time to fit residues: 71.1882 Evaluate side-chains 89 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.079537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065463 restraints weight = 18266.791| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.92 r_work: 0.2939 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 7620 Z= 0.280 Angle : 0.693 8.479 10378 Z= 0.361 Chirality : 0.048 0.195 1191 Planarity : 0.004 0.033 1314 Dihedral : 5.482 49.114 1104 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.99 % Allowed : 14.97 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: 0.17 (0.28), residues: 958 helix: -1.59 (0.84), residues: 31 sheet: 0.50 (0.24), residues: 466 loop : -0.05 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 54 TYR 0.015 0.002 TYR L 140 PHE 0.017 0.002 PHE H 154 TRP 0.008 0.001 TRP B 105 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 7606) covalent geometry : angle 0.68818 (10347) SS BOND : bond 0.00681 ( 11) SS BOND : angle 1.78131 ( 22) hydrogen bonds : bond 0.03494 ( 277) hydrogen bonds : angle 5.99544 ( 762) link_BETA1-4 : bond 0.00043 ( 1) link_BETA1-4 : angle 1.72540 ( 3) link_NAG-ASN : bond 0.00076 ( 2) link_NAG-ASN : angle 0.76583 ( 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 103 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9235 (mm110) cc_final: 0.8891 (mm110) REVERT: H 89 GLU cc_start: 0.8968 (pm20) cc_final: 0.8464 (pm20) REVERT: L 4 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: L 17 ASP cc_start: 0.8424 (m-30) cc_final: 0.8122 (m-30) REVERT: L 81 GLU cc_start: 0.9041 (mp0) cc_final: 0.8721 (pm20) REVERT: L 187 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8449 (mm-30) outliers start: 25 outliers final: 10 residues processed: 94 average time/residue: 0.6696 time to fit residues: 66.1237 Evaluate side-chains 84 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.081376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067315 restraints weight = 17956.285| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.92 r_work: 0.2973 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7620 Z= 0.159 Angle : 0.637 9.937 10378 Z= 0.331 Chirality : 0.046 0.187 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.353 50.763 1104 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.68 % Allowed : 17.01 % Favored : 81.32 % 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 aren not related in a simple way. whole: 0.21 (0.28), residues: 958 helix: -1.45 (0.86), residues: 31 sheet: 0.54 (0.24), residues: 460 loop : -0.04 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.019 0.001 TYR A 334 PHE 0.014 0.001 PHE H 154 TRP 0.008 0.001 TRP B 113 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7606) covalent geometry : angle 0.63404 (10347) SS BOND : bond 0.00522 ( 11) SS BOND : angle 1.41301 ( 22) hydrogen bonds : bond 0.03063 ( 277) hydrogen bonds : angle 5.73465 ( 762) link_BETA1-4 : bond 0.00133 ( 1) link_BETA1-4 : angle 1.55120 ( 3) link_NAG-ASN : bond 0.00208 ( 2) link_NAG-ASN : angle 0.81342 ( 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 94 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9169 (mm110) cc_final: 0.8872 (mm110) REVERT: B 207 ASN cc_start: 0.8360 (m-40) cc_final: 0.8095 (m-40) REVERT: H 89 GLU cc_start: 0.8794 (pm20) cc_final: 0.8300 (pm20) REVERT: H 220 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8555 (mp0) REVERT: L 17 ASP cc_start: 0.8316 (m-30) cc_final: 0.8048 (m-30) REVERT: L 81 GLU cc_start: 0.8988 (mp0) cc_final: 0.8735 (pm20) REVERT: L 187 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8305 (mm-30) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.6437 time to fit residues: 61.7307 Evaluate side-chains 85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 42 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067453 restraints weight = 18152.998| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.94 r_work: 0.2979 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7620 Z= 0.159 Angle : 0.630 9.010 10378 Z= 0.327 Chirality : 0.045 0.187 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.291 51.177 1104 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.56 % Allowed : 17.49 % Favored : 80.96 % 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 aren not related in a simple way. whole: 0.24 (0.28), residues: 958 helix: -1.39 (0.85), residues: 31 sheet: 0.54 (0.24), residues: 460 loop : -0.00 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.013 0.001 TYR L 140 PHE 0.012 0.001 PHE H 154 TRP 0.007 0.001 TRP B 113 HIS 0.003 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7606) covalent geometry : angle 0.62656 (10347) SS BOND : bond 0.00624 ( 11) SS BOND : angle 1.38435 ( 22) hydrogen bonds : bond 0.03003 ( 277) hydrogen bonds : angle 5.60400 ( 762) link_BETA1-4 : bond 0.00124 ( 1) link_BETA1-4 : angle 1.52417 ( 3) link_NAG-ASN : bond 0.00201 ( 2) link_NAG-ASN : angle 0.79139 ( 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 90 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9175 (mm110) cc_final: 0.8867 (mm110) REVERT: B 207 ASN cc_start: 0.8392 (m-40) cc_final: 0.8129 (m-40) REVERT: H 89 GLU cc_start: 0.8799 (pm20) cc_final: 0.8300 (pm20) REVERT: H 220 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8552 (mp0) REVERT: L 17 ASP cc_start: 0.8343 (m-30) cc_final: 0.8061 (m-30) REVERT: L 81 GLU cc_start: 0.9004 (mp0) cc_final: 0.8799 (pm20) REVERT: L 187 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8304 (mm-30) outliers start: 13 outliers final: 13 residues processed: 89 average time/residue: 0.6579 time to fit residues: 61.6443 Evaluate side-chains 85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.064404 restraints weight = 18257.885| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.91 r_work: 0.2915 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 7620 Z= 0.363 Angle : 0.761 9.849 10378 Z= 0.397 Chirality : 0.050 0.203 1191 Planarity : 0.005 0.042 1314 Dihedral : 5.673 48.788 1104 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.28 % Allowed : 17.37 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 aren not related in a simple way. whole: -0.07 (0.28), residues: 958 helix: -1.67 (0.80), residues: 31 sheet: 0.36 (0.23), residues: 468 loop : -0.24 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 54 TYR 0.030 0.002 TYR A 334 PHE 0.017 0.002 PHE B 156 TRP 0.012 0.002 TRP B 105 HIS 0.006 0.002 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00846 ( 7606) covalent geometry : angle 0.75629 (10347) SS BOND : bond 0.00783 ( 11) SS BOND : angle 1.96092 ( 22) hydrogen bonds : bond 0.03788 ( 277) hydrogen bonds : angle 6.11694 ( 762) link_BETA1-4 : bond 0.00031 ( 1) link_BETA1-4 : angle 1.82644 ( 3) link_NAG-ASN : bond 0.00156 ( 2) link_NAG-ASN : angle 0.87489 ( 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 92 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.9060 (m-80) cc_final: 0.8847 (m-80) REVERT: B 43 GLN cc_start: 0.9241 (mm110) cc_final: 0.8951 (mm110) REVERT: H 89 GLU cc_start: 0.8944 (pm20) cc_final: 0.8465 (pm20) REVERT: L 4 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8882 (mmm) REVERT: L 17 ASP cc_start: 0.8405 (m-30) cc_final: 0.8111 (m-30) REVERT: L 165 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8668 (mm-30) REVERT: L 187 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8327 (mm-30) outliers start: 19 outliers final: 11 residues processed: 86 average time/residue: 0.6575 time to fit residues: 59.4404 Evaluate side-chains 82 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067019 restraints weight = 17812.623| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.88 r_work: 0.2975 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7620 Z= 0.150 Angle : 0.650 9.110 10378 Z= 0.338 Chirality : 0.045 0.188 1191 Planarity : 0.004 0.040 1314 Dihedral : 5.383 51.296 1104 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.68 % Allowed : 17.84 % Favored : 80.48 % 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 aren not related in a simple way. whole: 0.15 (0.28), residues: 958 helix: -1.38 (0.82), residues: 31 sheet: 0.52 (0.24), residues: 467 loop : -0.13 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 16 TYR 0.014 0.001 TYR L 140 PHE 0.014 0.001 PHE H 154 TRP 0.010 0.001 TRP B 164 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7606) covalent geometry : angle 0.64697 (10347) SS BOND : bond 0.00608 ( 11) SS BOND : angle 1.38502 ( 22) hydrogen bonds : bond 0.03036 ( 277) hydrogen bonds : angle 5.67806 ( 762) link_BETA1-4 : bond 0.00255 ( 1) link_BETA1-4 : angle 1.53164 ( 3) link_NAG-ASN : bond 0.00234 ( 2) link_NAG-ASN : angle 0.87666 ( 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 92 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9168 (mm110) cc_final: 0.8886 (mm110) REVERT: H 89 GLU cc_start: 0.8776 (pm20) cc_final: 0.8312 (pm20) REVERT: L 17 ASP cc_start: 0.8335 (m-30) cc_final: 0.8045 (m-30) REVERT: L 187 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8258 (mm-30) outliers start: 14 outliers final: 11 residues processed: 90 average time/residue: 0.6229 time to fit residues: 58.9948 Evaluate side-chains 83 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 152 ASN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.080146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066080 restraints weight = 18165.263| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.92 r_work: 0.2951 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7620 Z= 0.214 Angle : 0.676 9.067 10378 Z= 0.352 Chirality : 0.047 0.194 1191 Planarity : 0.004 0.039 1314 Dihedral : 5.433 50.772 1104 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.68 % Allowed : 18.20 % Favored : 80.12 % 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 aren not related in a simple way. whole: 0.09 (0.28), residues: 958 helix: -1.29 (0.83), residues: 31 sheet: 0.49 (0.24), residues: 467 loop : -0.18 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.026 0.002 TYR A 334 PHE 0.014 0.001 PHE H 154 TRP 0.007 0.001 TRP B 113 HIS 0.004 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 7606) covalent geometry : angle 0.67211 (10347) SS BOND : bond 0.00651 ( 11) SS BOND : angle 1.57371 ( 22) hydrogen bonds : bond 0.03238 ( 277) hydrogen bonds : angle 5.73950 ( 762) link_BETA1-4 : bond 0.00100 ( 1) link_BETA1-4 : angle 1.62291 ( 3) link_NAG-ASN : bond 0.00096 ( 2) link_NAG-ASN : angle 0.82858 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.13 seconds wall clock time: 43 minutes 42.33 seconds (2622.33 seconds total)