Starting phenix.real_space_refine on Sun May 11 04:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9y_19016/05_2025/8r9y_19016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9y_19016/05_2025/8r9y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r9y_19016/05_2025/8r9y_19016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9y_19016/05_2025/8r9y_19016.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9y_19016/05_2025/8r9y_19016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9y_19016/05_2025/8r9y_19016.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.61, per 1000 atoms: 0.62 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.36 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: 2.26 Time building geometry restraints manager: 2.22 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: 1.730 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- 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 : 6.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (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 TRP 0.007 0.001 TRP C 94 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE H 154 TYR 0.011 0.001 TYR L 140 ARG 0.001 0.000 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.21495 ( 6) link_BETA1-4 : bond 0.00121 ( 1) link_BETA1-4 : angle 1.75226 ( 3) hydrogen bonds : bond 0.25154 ( 269) hydrogen bonds : angle 10.67525 ( 714) SS BOND : bond 0.00574 ( 11) SS BOND : angle 1.42534 ( 22) covalent geometry : bond 0.00316 ( 7611) covalent geometry : angle 0.58576 (10354) *********************** 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 : 0.772 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: 1.2844 time to fit residues: 210.4921 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 : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.085015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069725 restraints weight = 16727.530| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.14 r_work: 0.2961 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7625 Z= 0.162 Angle : 0.640 9.428 10385 Z= 0.332 Chirality : 0.045 0.139 1191 Planarity : 0.004 0.032 1315 Dihedral : 5.328 53.419 1105 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.91 % Allowed : 11.72 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.29), residues: 958 helix: -0.94 (0.85), residues: 31 sheet: 0.64 (0.25), residues: 470 loop : -0.21 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.005 0.001 HIS B 210 PHE 0.012 0.001 PHE H 154 TYR 0.010 0.001 TYR L 140 ARG 0.005 0.001 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 0.96256 ( 6) link_BETA1-4 : bond 0.00031 ( 1) link_BETA1-4 : angle 1.47683 ( 3) hydrogen bonds : bond 0.04278 ( 269) hydrogen bonds : angle 7.38560 ( 714) SS BOND : bond 0.00622 ( 11) SS BOND : angle 1.51597 ( 22) covalent geometry : bond 0.00369 ( 7611) covalent geometry : angle 0.63597 (10354) *********************** 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 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 THR cc_start: 0.8612 (m) cc_final: 0.8358 (p) REVERT: A 355 ASN cc_start: 0.8569 (m-40) cc_final: 0.8299 (p0) REVERT: A 412 GLN cc_start: 0.8790 (mm-40) cc_final: 0.7656 (tp-100) REVERT: B 73 ASP cc_start: 0.8128 (t0) cc_final: 0.7481 (t70) REVERT: B 222 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: C 18 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7740 (ttm-80) REVERT: C 109 THR cc_start: 0.8702 (m) cc_final: 0.8489 (p) REVERT: C 199 GLN cc_start: 0.8821 (tt0) cc_final: 0.8261 (tm-30) REVERT: H 13 GLN cc_start: 0.8830 (mp10) cc_final: 0.8136 (mp10) REVERT: H 89 GLU cc_start: 0.8575 (pm20) cc_final: 0.8292 (pm20) REVERT: H 103 MET cc_start: 0.7732 (mtp) cc_final: 0.7404 (mtp) REVERT: L 122 ASP cc_start: 0.8639 (p0) cc_final: 0.8003 (p0) REVERT: L 123 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7262 (mp0) REVERT: L 145 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8513 (tptp) REVERT: L 147 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: L 154 LEU cc_start: 0.8238 (mm) cc_final: 0.7987 (tt) REVERT: L 158 ASN cc_start: 0.8254 (t0) cc_final: 0.7998 (p0) REVERT: L 167 ASP cc_start: 0.8440 (t0) cc_final: 0.7869 (t70) REVERT: L 185 ASP cc_start: 0.8951 (m-30) cc_final: 0.8620 (t70) outliers start: 16 outliers final: 7 residues processed: 106 average time/residue: 1.1881 time to fit residues: 133.6283 Evaluate side-chains 97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 76 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.082743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067355 restraints weight = 17090.593| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.15 r_work: 0.2916 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1975 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= 0.247 Angle : 0.681 10.261 10385 Z= 0.350 Chirality : 0.048 0.176 1191 Planarity : 0.004 0.031 1315 Dihedral : 5.517 52.389 1105 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.59 % Allowed : 13.64 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 958 helix: -1.13 (0.82), residues: 31 sheet: 0.46 (0.24), residues: 471 loop : -0.27 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.005 0.001 HIS B 210 PHE 0.016 0.002 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.005 0.001 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 1.24423 ( 6) link_BETA1-4 : bond 0.00160 ( 1) link_BETA1-4 : angle 1.70707 ( 3) hydrogen bonds : bond 0.03816 ( 269) hydrogen bonds : angle 6.84830 ( 714) SS BOND : bond 0.00696 ( 11) SS BOND : angle 1.65514 ( 22) covalent geometry : bond 0.00577 ( 7611) covalent geometry : angle 0.67618 (10354) *********************** 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: 30 poor density : 92 time to evaluate : 0.858 Fit side-chains REVERT: A 353 THR cc_start: 0.8643 (m) cc_final: 0.8322 (p) REVERT: A 355 ASN cc_start: 0.8555 (m-40) cc_final: 0.8224 (p0) REVERT: A 370 ASN cc_start: 0.9058 (m-40) cc_final: 0.8839 (m110) REVERT: A 412 GLN cc_start: 0.8808 (mm-40) cc_final: 0.7698 (tp-100) REVERT: B 73 ASP cc_start: 0.8195 (t0) cc_final: 0.7538 (t70) REVERT: B 222 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7439 (pp20) REVERT: C 54 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.8057 (ttm170) REVERT: C 124 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: C 199 GLN cc_start: 0.8855 (tt0) cc_final: 0.8433 (tm-30) REVERT: H 13 GLN cc_start: 0.8834 (mp10) cc_final: 0.8167 (mp10) REVERT: H 89 GLU cc_start: 0.8579 (pm20) cc_final: 0.8259 (pm20) REVERT: H 103 MET cc_start: 0.7897 (mtp) cc_final: 0.7489 (mtp) REVERT: L 122 ASP cc_start: 0.8685 (p0) cc_final: 0.7996 (p0) REVERT: L 123 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7394 (mp0) REVERT: L 145 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8607 (tptp) REVERT: L 167 ASP cc_start: 0.8490 (t0) cc_final: 0.7920 (t70) REVERT: L 185 ASP cc_start: 0.8920 (m-30) cc_final: 0.8691 (t70) outliers start: 30 outliers final: 13 residues processed: 114 average time/residue: 1.0783 time to fit residues: 130.6708 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 60 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 180 THR 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 50 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 90 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 L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069887 restraints weight = 17180.654| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.15 r_work: 0.2991 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7625 Z= 0.139 Angle : 0.623 10.312 10385 Z= 0.318 Chirality : 0.045 0.161 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.329 53.281 1105 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.11 % Allowed : 16.27 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 958 helix: -0.79 (0.93), residues: 29 sheet: 0.51 (0.24), residues: 469 loop : -0.19 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.004 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 1.13908 ( 6) link_BETA1-4 : bond 0.00128 ( 1) link_BETA1-4 : angle 1.57284 ( 3) hydrogen bonds : bond 0.03098 ( 269) hydrogen bonds : angle 6.32107 ( 714) SS BOND : bond 0.00820 ( 11) SS BOND : angle 2.46081 ( 22) covalent geometry : bond 0.00323 ( 7611) covalent geometry : angle 0.61224 (10354) *********************** 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 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.895 Fit side-chains REVERT: A 412 GLN cc_start: 0.8777 (mm-40) cc_final: 0.7701 (tp-100) REVERT: B 73 ASP cc_start: 0.8232 (t0) cc_final: 0.7582 (t70) REVERT: B 222 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: C 199 GLN cc_start: 0.8811 (tt0) cc_final: 0.8503 (tm-30) REVERT: H 13 GLN cc_start: 0.8892 (mp10) cc_final: 0.8229 (mp10) REVERT: H 89 GLU cc_start: 0.8507 (pm20) cc_final: 0.8214 (pm20) REVERT: H 103 MET cc_start: 0.8009 (mtp) cc_final: 0.7607 (mtp) REVERT: L 31 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.7956 (t0) REVERT: L 122 ASP cc_start: 0.8611 (p0) cc_final: 0.7980 (p0) REVERT: L 123 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7442 (mp0) REVERT: L 125 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7227 (mm) REVERT: L 145 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8633 (tptp) REVERT: L 147 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: L 167 ASP cc_start: 0.8475 (t0) cc_final: 0.7939 (t70) outliers start: 26 outliers final: 12 residues processed: 114 average time/residue: 1.1076 time to fit residues: 134.1002 Evaluate side-chains 98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 0.0030 chunk 78 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 C 124 GLN H 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070413 restraints weight = 17147.467| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.14 r_work: 0.3002 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7625 Z= 0.130 Angle : 0.603 8.668 10385 Z= 0.309 Chirality : 0.045 0.157 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.214 53.192 1105 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.99 % Allowed : 17.22 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 958 helix: -0.80 (0.93), residues: 29 sheet: 0.56 (0.24), residues: 469 loop : -0.16 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE H 154 TYR 0.011 0.001 TYR L 140 ARG 0.003 0.000 ARG L 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 2) link_NAG-ASN : angle 1.09983 ( 6) link_BETA1-4 : bond 0.00132 ( 1) link_BETA1-4 : angle 1.54927 ( 3) hydrogen bonds : bond 0.02932 ( 269) hydrogen bonds : angle 6.02120 ( 714) SS BOND : bond 0.00657 ( 11) SS BOND : angle 2.05903 ( 22) covalent geometry : bond 0.00298 ( 7611) covalent geometry : angle 0.59527 (10354) *********************** 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 109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.055 Fit side-chains REVERT: A 412 GLN cc_start: 0.8766 (mm-40) cc_final: 0.7670 (tp-100) REVERT: B 73 ASP cc_start: 0.8247 (t0) cc_final: 0.7562 (t70) REVERT: B 222 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: C 199 GLN cc_start: 0.8797 (tt0) cc_final: 0.8464 (tm-30) REVERT: H 13 GLN cc_start: 0.8878 (mp10) cc_final: 0.8211 (mp10) REVERT: H 89 GLU cc_start: 0.8521 (pm20) cc_final: 0.8210 (pm20) REVERT: H 103 MET cc_start: 0.8005 (mtp) cc_final: 0.7606 (mtp) REVERT: L 31 ASN cc_start: 0.8569 (t0) cc_final: 0.8102 (t0) REVERT: L 122 ASP cc_start: 0.8601 (p0) cc_final: 0.7988 (p0) REVERT: L 125 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7269 (mm) REVERT: L 145 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8589 (tptp) REVERT: L 167 ASP cc_start: 0.8471 (t0) cc_final: 0.7938 (t70) outliers start: 25 outliers final: 15 residues processed: 105 average time/residue: 1.0302 time to fit residues: 115.5862 Evaluate side-chains 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 335 CYS 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 167 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 180 SER 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 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 12 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.091817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077293 restraints weight = 17034.747| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.96 r_work: 0.3191 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7625 Z= 0.117 Angle : 0.597 8.410 10385 Z= 0.306 Chirality : 0.045 0.146 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.135 53.243 1105 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.23 % Allowed : 18.06 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 958 helix: -0.60 (0.97), residues: 29 sheet: 0.61 (0.25), residues: 470 loop : -0.14 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE H 154 TYR 0.010 0.001 TYR L 140 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 1.06729 ( 6) link_BETA1-4 : bond 0.00001 ( 1) link_BETA1-4 : angle 1.48807 ( 3) hydrogen bonds : bond 0.02782 ( 269) hydrogen bonds : angle 5.83627 ( 714) SS BOND : bond 0.00637 ( 11) SS BOND : angle 1.84057 ( 22) covalent geometry : bond 0.00263 ( 7611) covalent geometry : angle 0.59089 (10354) *********************** 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 114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.878 Fit side-chains REVERT: A 412 GLN cc_start: 0.8697 (mm-40) cc_final: 0.7674 (tp-100) REVERT: B 73 ASP cc_start: 0.8312 (t0) cc_final: 0.7699 (t70) REVERT: H 13 GLN cc_start: 0.8904 (mp10) cc_final: 0.8251 (mp10) REVERT: H 89 GLU cc_start: 0.8382 (pm20) cc_final: 0.8175 (pm20) REVERT: H 103 MET cc_start: 0.8125 (mtp) cc_final: 0.7729 (mtp) REVERT: L 31 ASN cc_start: 0.8368 (t0) cc_final: 0.8075 (t0) REVERT: L 145 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8673 (tptp) REVERT: L 147 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: L 167 ASP cc_start: 0.8461 (t0) cc_final: 0.7995 (t70) outliers start: 27 outliers final: 16 residues processed: 109 average time/residue: 1.0648 time to fit residues: 123.6778 Evaluate side-chains 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 335 CYS 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 181 LEU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 180 SER 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 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 6 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 0.0010 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075847 restraints weight = 17077.935| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.95 r_work: 0.3175 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7625 Z= 0.161 Angle : 0.638 10.568 10385 Z= 0.324 Chirality : 0.046 0.227 1191 Planarity : 0.003 0.026 1315 Dihedral : 5.191 52.885 1105 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.35 % Allowed : 19.74 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 958 helix: -1.00 (0.88), residues: 29 sheet: 0.60 (0.24), residues: 470 loop : -0.17 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.011 0.001 TYR L 140 ARG 0.003 0.000 ARG L 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 2) link_NAG-ASN : angle 1.11029 ( 6) link_BETA1-4 : bond 0.00061 ( 1) link_BETA1-4 : angle 1.56855 ( 3) hydrogen bonds : bond 0.02919 ( 269) hydrogen bonds : angle 5.89748 ( 714) SS BOND : bond 0.00842 ( 11) SS BOND : angle 2.55093 ( 22) covalent geometry : bond 0.00378 ( 7611) covalent geometry : angle 0.62642 (10354) *********************** 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 106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.799 Fit side-chains REVERT: A 412 GLN cc_start: 0.8702 (mm-40) cc_final: 0.7676 (tp-100) REVERT: B 73 ASP cc_start: 0.8318 (t0) cc_final: 0.7709 (t70) REVERT: B 82 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: B 111 ASP cc_start: 0.9013 (p0) cc_final: 0.8791 (p0) REVERT: H 13 GLN cc_start: 0.8910 (mp10) cc_final: 0.8257 (mp10) REVERT: H 89 GLU cc_start: 0.8382 (pm20) cc_final: 0.8169 (pm20) REVERT: H 103 MET cc_start: 0.8173 (mtp) cc_final: 0.7817 (mtp) REVERT: L 1 ASP cc_start: 0.9024 (p0) cc_final: 0.8786 (p0) REVERT: L 3 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7764 (mm110) REVERT: L 31 ASN cc_start: 0.8416 (t0) cc_final: 0.8074 (t0) REVERT: L 145 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8658 (tptp) REVERT: L 147 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: L 167 ASP cc_start: 0.8476 (t0) cc_final: 0.7997 (t70) outliers start: 28 outliers final: 18 residues processed: 101 average time/residue: 1.0863 time to fit residues: 116.8004 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 335 CYS 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 82 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.089828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075072 restraints weight = 17262.091| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.97 r_work: 0.3153 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7625 Z= 0.185 Angle : 0.651 10.303 10385 Z= 0.332 Chirality : 0.046 0.216 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.283 52.923 1105 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.35 % Allowed : 20.45 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.29), residues: 958 helix: -1.24 (0.84), residues: 29 sheet: 0.53 (0.24), residues: 472 loop : -0.16 (0.32), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE H 154 TYR 0.012 0.001 TYR L 140 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 1.19704 ( 6) link_BETA1-4 : bond 0.00100 ( 1) link_BETA1-4 : angle 1.63570 ( 3) hydrogen bonds : bond 0.02975 ( 269) hydrogen bonds : angle 5.94901 ( 714) SS BOND : bond 0.00768 ( 11) SS BOND : angle 2.50322 ( 22) covalent geometry : bond 0.00436 ( 7611) covalent geometry : angle 0.64026 (10354) *********************** 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 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.831 Fit side-chains REVERT: A 333 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8537 (m) REVERT: A 412 GLN cc_start: 0.8722 (mm-40) cc_final: 0.7698 (tp-100) REVERT: B 73 ASP cc_start: 0.8308 (t0) cc_final: 0.7687 (t70) REVERT: B 82 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: H 13 GLN cc_start: 0.8916 (mp10) cc_final: 0.8270 (mp10) REVERT: H 87 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: H 103 MET cc_start: 0.8219 (mtp) cc_final: 0.7835 (mtp) REVERT: L 3 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7858 (mm110) REVERT: L 31 ASN cc_start: 0.8446 (t0) cc_final: 0.8063 (t0) REVERT: L 145 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8552 (tptp) REVERT: L 154 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8035 (tt) REVERT: L 167 ASP cc_start: 0.8501 (t0) cc_final: 0.8023 (t70) outliers start: 28 outliers final: 17 residues processed: 98 average time/residue: 1.1323 time to fit residues: 118.1241 Evaluate side-chains 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 335 CYS 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 82 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 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 134 CYS Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 154 LEU 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 4 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.090633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075842 restraints weight = 17453.725| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.99 r_work: 0.3166 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7625 Z= 0.152 Angle : 0.631 9.748 10385 Z= 0.322 Chirality : 0.046 0.189 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.233 53.244 1105 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.51 % Allowed : 21.17 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 958 helix: -1.17 (0.86), residues: 29 sheet: 0.59 (0.24), residues: 470 loop : -0.18 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 2) link_NAG-ASN : angle 1.19566 ( 6) link_BETA1-4 : bond 0.00014 ( 1) link_BETA1-4 : angle 1.58179 ( 3) hydrogen bonds : bond 0.02847 ( 269) hydrogen bonds : angle 5.84303 ( 714) SS BOND : bond 0.00730 ( 11) SS BOND : angle 2.35549 ( 22) covalent geometry : bond 0.00357 ( 7611) covalent geometry : angle 0.62134 (10354) *********************** 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 96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.811 Fit side-chains REVERT: A 333 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 412 GLN cc_start: 0.8708 (mm-40) cc_final: 0.7682 (tp-100) REVERT: B 73 ASP cc_start: 0.8323 (t0) cc_final: 0.7703 (t70) REVERT: B 82 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: H 13 GLN cc_start: 0.8921 (mp10) cc_final: 0.8269 (mp10) REVERT: H 87 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7230 (mtm-85) REVERT: H 103 MET cc_start: 0.8185 (mtp) cc_final: 0.7794 (mtp) REVERT: L 3 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7819 (mm110) REVERT: L 31 ASN cc_start: 0.8405 (t0) cc_final: 0.8045 (t0) REVERT: L 122 ASP cc_start: 0.8504 (p0) cc_final: 0.8278 (p0) REVERT: L 123 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7306 (mp0) REVERT: L 145 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8537 (tptp) REVERT: L 167 ASP cc_start: 0.8487 (t0) cc_final: 0.7994 (t70) outliers start: 21 outliers final: 15 residues processed: 93 average time/residue: 1.1404 time to fit residues: 112.9799 Evaluate side-chains 91 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 335 CYS 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 82 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL 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 134 CYS Chi-restraints excluded: chain L residue 145 LYS 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 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.089941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075158 restraints weight = 17446.569| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.99 r_work: 0.3154 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7625 Z= 0.177 Angle : 0.651 9.877 10385 Z= 0.331 Chirality : 0.046 0.187 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.279 53.012 1105 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.63 % Allowed : 21.53 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.29), residues: 958 helix: -1.25 (0.86), residues: 29 sheet: 0.55 (0.24), residues: 470 loop : -0.21 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE H 154 TYR 0.012 0.001 TYR L 140 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 1.23043 ( 6) link_BETA1-4 : bond 0.00041 ( 1) link_BETA1-4 : angle 1.64193 ( 3) hydrogen bonds : bond 0.02914 ( 269) hydrogen bonds : angle 5.88889 ( 714) SS BOND : bond 0.00748 ( 11) SS BOND : angle 2.39223 ( 22) covalent geometry : bond 0.00417 ( 7611) covalent geometry : angle 0.64135 (10354) ********************** 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 97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.857 Fit side-chains REVERT: A 333 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8558 (m) REVERT: A 412 GLN cc_start: 0.8708 (mm-40) cc_final: 0.7678 (tp-100) REVERT: B 73 ASP cc_start: 0.8314 (t0) cc_final: 0.7691 (t70) REVERT: B 82 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: H 13 GLN cc_start: 0.8920 (mp10) cc_final: 0.8268 (mp10) REVERT: H 87 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7697 (ptp-110) REVERT: H 103 MET cc_start: 0.8191 (mtp) cc_final: 0.7799 (mtp) REVERT: L 31 ASN cc_start: 0.8435 (t0) cc_final: 0.8043 (t0) REVERT: L 122 ASP cc_start: 0.8501 (p0) cc_final: 0.8292 (p0) REVERT: L 123 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7340 (mp0) REVERT: L 145 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8547 (tptp) REVERT: L 167 ASP cc_start: 0.8501 (t0) cc_final: 0.8016 (t70) outliers start: 22 outliers final: 16 residues processed: 94 average time/residue: 1.0837 time to fit residues: 108.6913 Evaluate side-chains 92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 335 CYS 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 82 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain H residue 11 VAL 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 134 CYS Chi-restraints excluded: chain L residue 145 LYS 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 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.089524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074793 restraints weight = 17296.258| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.96 r_work: 0.3148 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7625 Z= 0.194 Angle : 0.658 9.888 10385 Z= 0.337 Chirality : 0.046 0.179 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.356 52.999 1105 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.63 % Allowed : 21.41 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.29), residues: 958 helix: -1.23 (0.88), residues: 29 sheet: 0.53 (0.24), residues: 469 loop : -0.22 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.003 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 2) link_NAG-ASN : angle 1.27789 ( 6) link_BETA1-4 : bond 0.00205 ( 1) link_BETA1-4 : angle 1.67602 ( 3) hydrogen bonds : bond 0.02981 ( 269) hydrogen bonds : angle 5.94495 ( 714) SS BOND : bond 0.00748 ( 11) SS BOND : angle 2.39726 ( 22) covalent geometry : bond 0.00458 ( 7611) covalent geometry : angle 0.64848 (10354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4518.68 seconds wall clock time: 78 minutes 58.26 seconds (4738.26 seconds total)