Starting phenix.real_space_refine on Wed Mar 12 07:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9y_19016/03_2025/8r9y_19016.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9y_19016/03_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_19016/03_2025/8r9y_19016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9y_19016/03_2025/8r9y_19016.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9y_19016/03_2025/8r9y_19016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9y_19016/03_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-5624/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: 4.82, per 1000 atoms: 0.65 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: 1.68 Conformation dependent library (CDL) restraints added in 993.4 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 23 sheets defined 5.9% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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: 2.25 Time building geometry restraints manager: 2.03 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: 2.410 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: 0.050 Set scattering table: 0.070 Process input model: 21.280 Find NCS groups from input model: 0.130 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- 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 7611 Z= 0.204 Angle : 0.586 12.471 10354 Z= 0.296 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 *********************** 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 : 0.844 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: 1.3503 time to fit residues: 221.2561 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 : 0.801 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.085028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069822 restraints weight = 16745.497| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.13 r_work: 0.2962 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7611 Z= 0.235 Angle : 0.636 9.412 10354 Z= 0.331 Chirality : 0.046 0.143 1191 Planarity : 0.004 0.032 1315 Dihedral : 5.326 53.319 1105 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.91 % Allowed : 11.84 % Favored : 86.24 % 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: -0.90 (0.85), residues: 31 sheet: 0.65 (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 B 164 HIS 0.005 0.001 HIS C 189 PHE 0.012 0.001 PHE H 154 TYR 0.009 0.001 TYR L 140 ARG 0.005 0.001 ARG C 54 *********************** 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 114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 THR cc_start: 0.8616 (m) cc_final: 0.8373 (p) REVERT: A 355 ASN cc_start: 0.8582 (m-40) cc_final: 0.8327 (p0) REVERT: A 370 ASN cc_start: 0.9046 (m-40) cc_final: 0.8830 (m110) REVERT: A 412 GLN cc_start: 0.8790 (mm-40) cc_final: 0.7664 (tp-100) REVERT: B 73 ASP cc_start: 0.8135 (t0) cc_final: 0.7494 (t70) REVERT: B 222 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: C 18 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7750 (ttm-80) REVERT: C 109 THR cc_start: 0.8706 (m) cc_final: 0.8494 (p) REVERT: C 199 GLN cc_start: 0.8818 (tt0) cc_final: 0.8268 (tm-30) REVERT: H 13 GLN cc_start: 0.8840 (mp10) cc_final: 0.8148 (mp10) REVERT: H 89 GLU cc_start: 0.8565 (pm20) cc_final: 0.8219 (pm20) REVERT: H 103 MET cc_start: 0.7761 (mtp) cc_final: 0.7432 (mtp) REVERT: L 122 ASP cc_start: 0.8639 (p0) cc_final: 0.8006 (p0) REVERT: L 123 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7265 (mp0) REVERT: L 145 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8517 (tptp) REVERT: L 147 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: L 154 LEU cc_start: 0.8225 (mm) cc_final: 0.7971 (tt) REVERT: L 158 ASN cc_start: 0.8253 (t0) cc_final: 0.8004 (p0) REVERT: L 167 ASP cc_start: 0.8443 (t0) cc_final: 0.7879 (t70) REVERT: L 185 ASP cc_start: 0.8949 (m-30) cc_final: 0.8620 (t70) outliers start: 16 outliers final: 7 residues processed: 107 average time/residue: 1.2476 time to fit residues: 141.3753 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 : 0.939 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.081509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066151 restraints weight = 17258.641| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.14 r_work: 0.2891 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 7611 Z= 0.486 Angle : 0.738 11.128 10354 Z= 0.383 Chirality : 0.050 0.209 1191 Planarity : 0.004 0.033 1315 Dihedral : 5.741 51.926 1105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.95 % Allowed : 14.35 % Favored : 81.70 % 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 (0.28), residues: 958 helix: -1.35 (0.79), residues: 31 sheet: 0.36 (0.24), residues: 471 loop : -0.39 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 36 HIS 0.007 0.002 HIS B 210 PHE 0.019 0.002 PHE H 154 TYR 0.015 0.002 TYR L 140 ARG 0.005 0.001 ARG C 54 *********************** 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 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.891 Fit side-chains REVERT: A 355 ASN cc_start: 0.8603 (m-40) cc_final: 0.8388 (m-40) REVERT: A 412 GLN cc_start: 0.8808 (mm-40) cc_final: 0.7655 (tp-100) REVERT: B 73 ASP cc_start: 0.8178 (t0) cc_final: 0.7477 (t70) REVERT: B 222 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: C 54 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.8045 (ttm170) REVERT: C 199 GLN cc_start: 0.8839 (tt0) cc_final: 0.8450 (tm-30) REVERT: H 13 GLN cc_start: 0.8852 (mp10) cc_final: 0.8201 (mp10) REVERT: H 89 GLU cc_start: 0.8578 (pm20) cc_final: 0.8263 (pm20) REVERT: L 122 ASP cc_start: 0.8698 (p0) cc_final: 0.8056 (p0) REVERT: L 123 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7479 (mp0) REVERT: L 145 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8629 (tptp) REVERT: L 154 LEU cc_start: 0.8435 (mm) cc_final: 0.8181 (tt) REVERT: L 158 ASN cc_start: 0.8227 (t0) cc_final: 0.8025 (p0) REVERT: L 167 ASP cc_start: 0.8486 (t0) cc_final: 0.7911 (t70) REVERT: L 185 ASP cc_start: 0.8940 (m-30) cc_final: 0.8729 (t70) outliers start: 33 outliers final: 12 residues processed: 112 average time/residue: 1.1281 time to fit residues: 134.2218 Evaluate side-chains 91 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.0370 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 63 ASN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070498 restraints weight = 17159.020| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.16 r_work: 0.3001 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 7611 Z= 0.173 Angle : 0.597 7.991 10354 Z= 0.309 Chirality : 0.045 0.146 1191 Planarity : 0.003 0.030 1315 Dihedral : 5.328 53.776 1105 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: 0.11 (0.29), residues: 958 helix: -0.86 (0.91), residues: 29 sheet: 0.47 (0.24), residues: 469 loop : -0.18 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE H 154 TYR 0.014 0.001 TYR L 140 ARG 0.004 0.000 ARG C 54 *********************** 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 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 353 THR cc_start: 0.8613 (m) cc_final: 0.8391 (p) REVERT: A 412 GLN cc_start: 0.8768 (mm-40) cc_final: 0.7652 (tp-100) REVERT: B 73 ASP cc_start: 0.8204 (t0) cc_final: 0.7519 (t70) REVERT: C 199 GLN cc_start: 0.8773 (tt0) cc_final: 0.8512 (tm-30) REVERT: H 13 GLN cc_start: 0.8874 (mp10) cc_final: 0.8210 (mp10) REVERT: H 87 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7778 (mtm-85) REVERT: H 89 GLU cc_start: 0.8475 (pm20) cc_final: 0.8226 (pm20) REVERT: H 103 MET cc_start: 0.7966 (mtp) cc_final: 0.7685 (mtp) REVERT: L 31 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7922 (t0) REVERT: L 122 ASP cc_start: 0.8582 (p0) cc_final: 0.8023 (p0) REVERT: L 145 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8552 (tptp) REVERT: L 167 ASP cc_start: 0.8466 (t0) cc_final: 0.7929 (t70) outliers start: 25 outliers final: 11 residues processed: 115 average time/residue: 1.1044 time to fit residues: 134.6750 Evaluate side-chains 94 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 211 LYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 181 LEU 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 145 LYS 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: 0.9990 chunk 19 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN H 179 GLN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069465 restraints weight = 17173.959| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.15 r_work: 0.2981 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7611 Z= 0.247 Angle : 0.627 8.395 10354 Z= 0.321 Chirality : 0.046 0.238 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.312 53.037 1105 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.35 % Allowed : 17.11 % Favored : 79.55 % 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: 0.07 (0.28), residues: 958 helix: -1.13 (0.87), residues: 29 sheet: 0.46 (0.24), residues: 469 loop : -0.21 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.012 0.001 TYR L 140 ARG 0.005 0.000 ARG L 142 *********************** 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 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 353 THR cc_start: 0.8670 (m) cc_final: 0.8300 (p) REVERT: A 412 GLN cc_start: 0.8771 (mm-40) cc_final: 0.7655 (tp-100) REVERT: B 73 ASP cc_start: 0.8245 (t0) cc_final: 0.7566 (t70) REVERT: B 82 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: C 199 GLN cc_start: 0.8791 (tt0) cc_final: 0.8479 (tm-30) REVERT: H 13 GLN cc_start: 0.8885 (mp10) cc_final: 0.8226 (mp10) REVERT: H 89 GLU cc_start: 0.8501 (pm20) cc_final: 0.8187 (pm20) REVERT: H 103 MET cc_start: 0.8047 (mtp) cc_final: 0.7730 (mtp) REVERT: L 31 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8125 (t0) REVERT: L 145 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8591 (tptp) REVERT: L 167 ASP cc_start: 0.8494 (t0) cc_final: 0.7950 (t70) outliers start: 28 outliers final: 17 residues processed: 105 average time/residue: 1.1182 time to fit residues: 124.9250 Evaluate side-chains 98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 211 LYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 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: 2.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 63 ASN C 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070143 restraints weight = 17148.678| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.14 r_work: 0.2997 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 7611 Z= 0.199 Angle : 0.603 7.605 10354 Z= 0.311 Chirality : 0.045 0.160 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.236 53.301 1105 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.59 % Allowed : 18.06 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.28), residues: 958 helix: -1.02 (0.90), residues: 29 sheet: 0.56 (0.24), residues: 468 loop : -0.25 (0.32), residues: 461 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 0.011 0.001 PHE H 154 TYR 0.012 0.001 TYR L 140 ARG 0.003 0.000 ARG L 142 *********************** 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 116 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 353 THR cc_start: 0.8554 (m) cc_final: 0.8312 (p) REVERT: A 412 GLN cc_start: 0.8758 (mm-40) cc_final: 0.7658 (tp-100) REVERT: B 73 ASP cc_start: 0.8242 (t0) cc_final: 0.7557 (t70) REVERT: B 82 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: C 199 GLN cc_start: 0.8749 (tt0) cc_final: 0.8474 (tm-30) REVERT: H 13 GLN cc_start: 0.8888 (mp10) cc_final: 0.8228 (mp10) REVERT: H 89 GLU cc_start: 0.8498 (pm20) cc_final: 0.8208 (pm20) REVERT: L 1 ASP cc_start: 0.9050 (p0) cc_final: 0.8734 (p0) REVERT: L 3 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7801 (mm110) REVERT: L 31 ASN cc_start: 0.8520 (t0) cc_final: 0.8119 (t0) REVERT: L 122 ASP cc_start: 0.8754 (p0) cc_final: 0.8516 (p0) REVERT: L 123 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7343 (mp0) REVERT: L 145 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8635 (tptp) REVERT: L 167 ASP cc_start: 0.8493 (t0) cc_final: 0.7942 (t70) outliers start: 30 outliers final: 19 residues processed: 107 average time/residue: 1.1405 time to fit residues: 129.8054 Evaluate side-chains 102 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 B residue 211 LYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 91 THR 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 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 0.0070 chunk 50 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.091773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077111 restraints weight = 16943.930| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.97 r_work: 0.3190 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7611 Z= 0.172 Angle : 0.598 8.906 10354 Z= 0.305 Chirality : 0.045 0.250 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.130 53.412 1105 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.99 % Allowed : 19.38 % Favored : 77.63 % 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: -1.05 (0.89), residues: 29 sheet: 0.64 (0.24), residues: 467 loop : -0.19 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE H 154 TYR 0.011 0.001 TYR L 140 ARG 0.003 0.000 ARG L 142 *********************** 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 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8690 (mm-40) cc_final: 0.7664 (tp-100) REVERT: B 73 ASP cc_start: 0.8301 (t0) cc_final: 0.7691 (t70) REVERT: B 111 ASP cc_start: 0.9011 (p0) cc_final: 0.8797 (p0) REVERT: C 199 GLN cc_start: 0.8678 (tt0) cc_final: 0.8473 (tm-30) REVERT: H 13 GLN cc_start: 0.8906 (mp10) cc_final: 0.8250 (mp10) REVERT: H 89 GLU cc_start: 0.8404 (pm20) cc_final: 0.8192 (pm20) REVERT: L 1 ASP cc_start: 0.8978 (p0) cc_final: 0.8709 (p0) REVERT: L 3 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7813 (mm110) REVERT: L 31 ASN cc_start: 0.8323 (t0) cc_final: 0.8058 (t0) REVERT: L 122 ASP cc_start: 0.8579 (p0) cc_final: 0.8360 (p0) REVERT: L 123 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7331 (mp0) REVERT: L 147 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: L 161 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8060 (tp30) REVERT: L 167 ASP cc_start: 0.8475 (t0) cc_final: 0.7991 (t70) outliers start: 25 outliers final: 19 residues processed: 109 average time/residue: 1.1320 time to fit residues: 131.0951 Evaluate side-chains 99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 211 LYS 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 C residue 206 THR Chi-restraints excluded: chain H residue 91 THR 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 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: 1.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 0.0060 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.091181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.077019 restraints weight = 17348.654| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.86 r_work: 0.3133 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7611 Z= 0.190 Angle : 0.599 7.389 10354 Z= 0.307 Chirality : 0.045 0.213 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.127 53.265 1105 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.99 % Allowed : 20.57 % Favored : 76.44 % 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: 0.25 (0.29), residues: 958 helix: -1.10 (0.89), residues: 29 sheet: 0.67 (0.24), residues: 467 loop : -0.20 (0.32), residues: 462 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 0.012 0.001 TYR L 140 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 412 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7655 (tp-100) REVERT: B 73 ASP cc_start: 0.8326 (t0) cc_final: 0.7699 (t70) REVERT: B 111 ASP cc_start: 0.9010 (p0) cc_final: 0.8799 (p0) REVERT: C 199 GLN cc_start: 0.8690 (tt0) cc_final: 0.8475 (tm-30) REVERT: H 13 GLN cc_start: 0.8915 (mp10) cc_final: 0.8233 (mp10) REVERT: H 89 GLU cc_start: 0.8395 (pm20) cc_final: 0.8153 (pm20) REVERT: L 31 ASN cc_start: 0.8334 (t0) cc_final: 0.8043 (t0) REVERT: L 123 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7355 (mp0) REVERT: L 161 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8019 (tp30) REVERT: L 167 ASP cc_start: 0.8471 (t0) cc_final: 0.7968 (t70) outliers start: 25 outliers final: 18 residues processed: 95 average time/residue: 1.1796 time to fit residues: 119.1556 Evaluate side-chains 92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 211 LYS 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 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 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: 0.1980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.089722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075436 restraints weight = 17650.005| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.88 r_work: 0.3104 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7611 Z= 0.257 Angle : 0.632 8.872 10354 Z= 0.322 Chirality : 0.046 0.199 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.242 52.977 1105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.75 % Allowed : 20.69 % Favored : 76.56 % 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: 0.17 (0.29), residues: 958 helix: -1.15 (0.89), residues: 29 sheet: 0.60 (0.24), residues: 468 loop : -0.23 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.001 PHE H 154 TYR 0.012 0.001 TYR L 140 ARG 0.004 0.000 ARG H 87 *********************** 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 98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 333 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8533 (m) REVERT: A 412 GLN cc_start: 0.8686 (mm-40) cc_final: 0.7652 (tp-100) REVERT: B 73 ASP cc_start: 0.8312 (t0) cc_final: 0.7681 (t70) REVERT: H 13 GLN cc_start: 0.8878 (mp10) cc_final: 0.8209 (mp10) REVERT: H 87 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7492 (mtt-85) REVERT: H 89 GLU cc_start: 0.8403 (pm20) cc_final: 0.8193 (pm20) REVERT: L 31 ASN cc_start: 0.8392 (t0) cc_final: 0.8055 (t0) REVERT: L 122 ASP cc_start: 0.8680 (p0) cc_final: 0.8390 (p0) REVERT: L 123 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7402 (mp0) REVERT: L 167 ASP cc_start: 0.8474 (t0) cc_final: 0.7953 (t70) outliers start: 23 outliers final: 20 residues processed: 94 average time/residue: 1.0806 time to fit residues: 108.4154 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 : 0.890 ------------------------------------------------------------------------------- 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 211 LYS Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 167 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 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 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: 0.3980 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.089863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075526 restraints weight = 17653.710| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.88 r_work: 0.3108 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 7611 Z= 0.276 Angle : 0.992 61.600 10354 Z= 0.466 Chirality : 0.050 0.657 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.252 52.984 1105 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 21.29 % Favored : 76.08 % Cbeta Deviations : 0.11 % 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: 0.16 (0.29), residues: 958 helix: -1.14 (0.89), residues: 29 sheet: 0.60 (0.24), residues: 468 loop : -0.24 (0.32), residues: 461 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 H 87 ********************** 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 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 333 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8531 (m) REVERT: A 412 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7651 (tp-100) REVERT: B 73 ASP cc_start: 0.8305 (t0) cc_final: 0.7670 (t70) REVERT: H 13 GLN cc_start: 0.8874 (mp10) cc_final: 0.8206 (mp10) REVERT: H 87 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7065 (mtm-85) REVERT: H 89 GLU cc_start: 0.8405 (pm20) cc_final: 0.8188 (pm20) REVERT: L 31 ASN cc_start: 0.8397 (t0) cc_final: 0.8056 (t0) REVERT: L 122 ASP cc_start: 0.8678 (p0) cc_final: 0.8245 (p0) REVERT: L 167 ASP cc_start: 0.8473 (t0) cc_final: 0.7958 (t70) outliers start: 22 outliers final: 19 residues processed: 90 average time/residue: 1.1298 time to fit residues: 108.5965 Evaluate side-chains 92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 211 LYS 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 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 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: 0.5980 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.090323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076120 restraints weight = 17412.198| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.85 r_work: 0.3115 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7611 Z= 0.221 Angle : 0.629 7.464 10354 Z= 0.324 Chirality : 0.046 0.188 1191 Planarity : 0.003 0.027 1315 Dihedral : 5.254 53.179 1105 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.75 % Allowed : 21.29 % 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: 0.16 (0.29), residues: 958 helix: -1.10 (0.89), residues: 29 sheet: 0.60 (0.24), residues: 468 loop : -0.25 (0.32), residues: 461 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 0.013 0.001 PHE H 154 TYR 0.012 0.001 TYR L 140 ARG 0.003 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4460.30 seconds wall clock time: 77 minutes 22.21 seconds (4642.21 seconds total)