Starting phenix.real_space_refine on Fri Jul 19 10:18:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9y_19016/07_2024/8r9y_19016.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9y_19016/07_2024/8r9y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9y_19016/07_2024/8r9y_19016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9y_19016/07_2024/8r9y_19016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9y_19016/07_2024/8r9y_19016.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9y_19016/07_2024/8r9y_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 Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.30, per 1000 atoms: 0.71 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 - 3.50 Amino acid : False - 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 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: 1.33 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: 2.36 Time building geometry restraints manager: 3.24 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: 99.54 - 106.44: 236 106.44 - 113.34: 4209 113.34 - 120.24: 2423 120.24 - 127.14: 3389 127.14 - 134.03: 97 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 2.440 nonbonded pdb=" OE1 GLN B 62 " pdb=" NH1 ARG B 65 " model vdw 2.266 2.520 nonbonded pdb=" O PRO H 131 " pdb=" OG SER L 121 " model vdw 2.268 2.440 nonbonded pdb=" OE2 GLU A 410 " pdb=" NH1 ARG H 99 " model vdw 2.311 2.520 nonbonded pdb=" O SER B 77 " pdb=" OG SER B 77 " model vdw 2.321 2.440 ... (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 ========== 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: 1.940 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.873 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: 1.3123 time to fit residues: 215.1864 Evaluate side-chains 85 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7611 Z= 0.224 Angle : 0.620 9.304 10354 Z= 0.319 Chirality : 0.045 0.138 1191 Planarity : 0.004 0.027 1315 Dihedral : 5.299 53.526 1105 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.15 % Allowed : 11.60 % 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: -0.95 (0.84), 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 0.010 0.001 TYR H 95 ARG 0.005 0.000 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 117 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 THR cc_start: 0.8594 (m) cc_final: 0.8320 (p) REVERT: A 355 ASN cc_start: 0.8563 (m-40) cc_final: 0.8302 (p0) REVERT: A 412 GLN cc_start: 0.8681 (mm-40) cc_final: 0.7553 (tp-100) REVERT: B 73 ASP cc_start: 0.7954 (t0) cc_final: 0.7301 (t70) REVERT: B 99 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 222 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: C 18 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7597 (ttm-80) REVERT: C 199 GLN cc_start: 0.8845 (tt0) cc_final: 0.8373 (tm-30) REVERT: H 13 GLN cc_start: 0.8792 (mp10) cc_final: 0.8092 (mp10) REVERT: H 89 GLU cc_start: 0.8182 (pm20) cc_final: 0.7935 (pm20) REVERT: H 103 MET cc_start: 0.7784 (mtp) cc_final: 0.7448 (mtp) REVERT: L 27 GLN cc_start: 0.8026 (mt0) cc_final: 0.7804 (mt0) REVERT: L 81 GLU cc_start: 0.8654 (pm20) cc_final: 0.8434 (pm20) REVERT: L 145 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8495 (tptp) REVERT: L 147 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: L 154 LEU cc_start: 0.8197 (mm) cc_final: 0.7942 (tt) REVERT: L 158 ASN cc_start: 0.8195 (t0) cc_final: 0.7885 (p0) REVERT: L 167 ASP cc_start: 0.8374 (t0) cc_final: 0.7770 (t70) REVERT: L 185 ASP cc_start: 0.8962 (m-30) cc_final: 0.8645 (t70) outliers start: 18 outliers final: 10 residues processed: 109 average time/residue: 1.1535 time to fit residues: 133.2871 Evaluate side-chains 99 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 145 LYS Chi-restraints excluded: chain L residue 147 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 0.0570 chunk 68 optimal weight: 0.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- 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 3 GLN H 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7611 Z= 0.338 Angle : 0.651 10.181 10354 Z= 0.335 Chirality : 0.046 0.159 1191 Planarity : 0.004 0.030 1315 Dihedral : 5.441 52.552 1105 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.31 % Allowed : 13.88 % Favored : 81.82 % 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: 0.10 (0.29), residues: 958 helix: -1.09 (0.83), residues: 31 sheet: 0.53 (0.24), residues: 471 loop : -0.25 (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 0.012 0.001 TYR L 140 ARG 0.005 0.000 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 124 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 0.872 Fit side-chains REVERT: A 353 THR cc_start: 0.8640 (m) cc_final: 0.8290 (p) REVERT: A 355 ASN cc_start: 0.8517 (m-40) cc_final: 0.8202 (p0) REVERT: A 412 GLN cc_start: 0.8683 (mm-40) cc_final: 0.7562 (tp-100) REVERT: B 73 ASP cc_start: 0.7953 (t0) cc_final: 0.7244 (t70) REVERT: B 222 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: C 54 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.8028 (ttm170) REVERT: C 199 GLN cc_start: 0.8893 (tt0) cc_final: 0.8436 (tm-30) REVERT: H 13 GLN cc_start: 0.8807 (mp10) cc_final: 0.8129 (mp10) REVERT: H 89 GLU cc_start: 0.8232 (pm20) cc_final: 0.7953 (pm20) REVERT: H 103 MET cc_start: 0.7894 (mtp) cc_final: 0.7542 (mtp) REVERT: L 27 GLN cc_start: 0.8038 (mt0) cc_final: 0.7828 (mt0) REVERT: L 125 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7279 (mm) REVERT: L 145 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8541 (tptp) REVERT: L 158 ASN cc_start: 0.8180 (t0) cc_final: 0.7949 (p0) REVERT: L 167 ASP cc_start: 0.8472 (t0) cc_final: 0.7892 (t70) REVERT: L 185 ASP cc_start: 0.8931 (m-30) cc_final: 0.8703 (t70) outliers start: 36 outliers final: 19 residues processed: 112 average time/residue: 1.0980 time to fit residues: 131.0766 Evaluate side-chains 101 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 222 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 185 ASP Chi-restraints excluded: chain H residue 53 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 ASN C 124 GLN L 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7611 Z= 0.227 Angle : 0.609 8.076 10354 Z= 0.310 Chirality : 0.045 0.165 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.330 53.163 1105 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.43 % Allowed : 14.95 % 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: -1.18 (0.86), residues: 31 sheet: 0.54 (0.24), residues: 471 loop : -0.19 (0.32), residues: 456 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 0.014 0.001 PHE H 154 TYR 0.013 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 126 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 89 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 353 THR cc_start: 0.8507 (m) cc_final: 0.8224 (p) REVERT: A 355 ASN cc_start: 0.8539 (m-40) cc_final: 0.8331 (m-40) REVERT: A 412 GLN cc_start: 0.8666 (mm-40) cc_final: 0.7518 (tp-100) REVERT: B 73 ASP cc_start: 0.7939 (t0) cc_final: 0.7241 (t70) REVERT: B 222 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: C 54 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.8013 (ttm170) REVERT: C 199 GLN cc_start: 0.8885 (tt0) cc_final: 0.8502 (tm-30) REVERT: H 13 GLN cc_start: 0.8801 (mp10) cc_final: 0.8109 (mp10) REVERT: H 89 GLU cc_start: 0.8193 (pm20) cc_final: 0.7925 (pm20) REVERT: H 103 MET cc_start: 0.7859 (mtp) cc_final: 0.7492 (mtp) REVERT: L 27 GLN cc_start: 0.8050 (mt0) cc_final: 0.7843 (mt0) REVERT: L 31 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8041 (t0) REVERT: L 125 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7222 (mm) REVERT: L 145 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8481 (tptp) REVERT: L 167 ASP cc_start: 0.8463 (t0) cc_final: 0.7877 (t70) outliers start: 37 outliers final: 23 residues processed: 115 average time/residue: 1.1782 time to fit residues: 144.5249 Evaluate side-chains 104 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 222 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 185 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7611 Z= 0.266 Angle : 0.617 7.887 10354 Z= 0.315 Chirality : 0.045 0.167 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.331 52.943 1105 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.67 % Allowed : 16.51 % Favored : 78.83 % 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 (0.28), residues: 958 helix: -1.29 (0.86), residues: 31 sheet: 0.53 (0.24), residues: 471 loop : -0.22 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 94 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 0.003 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 118 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 79 time to evaluate : 0.908 Fit side-chains REVERT: A 353 THR cc_start: 0.8490 (m) cc_final: 0.8201 (p) REVERT: A 355 ASN cc_start: 0.8512 (m-40) cc_final: 0.8295 (m-40) REVERT: A 412 GLN cc_start: 0.8661 (mm-40) cc_final: 0.7519 (tp-100) REVERT: B 73 ASP cc_start: 0.7986 (t0) cc_final: 0.7288 (t70) REVERT: B 82 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: B 222 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: C 54 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.8047 (ttm170) REVERT: C 199 GLN cc_start: 0.8869 (tt0) cc_final: 0.8465 (tm-30) REVERT: H 13 GLN cc_start: 0.8801 (mp10) cc_final: 0.8102 (mp10) REVERT: L 27 GLN cc_start: 0.7974 (mt0) cc_final: 0.7742 (mt0) REVERT: L 31 ASN cc_start: 0.8716 (t0) cc_final: 0.8115 (t0) REVERT: L 125 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7104 (mm) REVERT: L 154 LEU cc_start: 0.8162 (mm) cc_final: 0.7917 (tt) REVERT: L 167 ASP cc_start: 0.8472 (t0) cc_final: 0.7892 (t70) outliers start: 39 outliers final: 23 residues processed: 108 average time/residue: 1.1029 time to fit residues: 126.8760 Evaluate side-chains 103 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 58 GLU 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 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 81 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7611 Z= 0.303 Angle : 0.634 7.736 10354 Z= 0.324 Chirality : 0.046 0.184 1191 Planarity : 0.003 0.030 1315 Dihedral : 5.396 52.868 1105 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.55 % Allowed : 17.46 % Favored : 77.99 % 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: -1.34 (0.86), residues: 31 sheet: 0.48 (0.24), residues: 471 loop : -0.28 (0.32), residues: 456 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 0.015 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.004 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 fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 0.794 Fit side-chains REVERT: A 353 THR cc_start: 0.8482 (m) cc_final: 0.8222 (p) REVERT: A 412 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7556 (tp-100) REVERT: B 73 ASP cc_start: 0.7988 (t0) cc_final: 0.7277 (t70) REVERT: B 82 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: B 222 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7449 (pp20) REVERT: C 199 GLN cc_start: 0.8858 (tt0) cc_final: 0.8482 (tm-30) REVERT: H 13 GLN cc_start: 0.8795 (mp10) cc_final: 0.8096 (mp10) REVERT: L 31 ASN cc_start: 0.8646 (t0) cc_final: 0.8078 (t0) REVERT: L 123 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7548 (mp0) REVERT: L 125 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7090 (mm) REVERT: L 154 LEU cc_start: 0.8186 (mm) cc_final: 0.7926 (tt) REVERT: L 167 ASP cc_start: 0.8490 (t0) cc_final: 0.7895 (t70) outliers start: 38 outliers final: 25 residues processed: 105 average time/residue: 1.1315 time to fit residues: 126.4106 Evaluate side-chains 103 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 58 GLU 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 179 LEU 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 10 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7611 Z= 0.243 Angle : 0.611 8.199 10354 Z= 0.312 Chirality : 0.045 0.166 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.317 53.334 1105 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.47 % Allowed : 19.02 % Favored : 77.51 % 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: 0.09 (0.28), residues: 958 helix: -1.14 (0.91), residues: 31 sheet: 0.55 (0.24), residues: 469 loop : -0.28 (0.32), residues: 458 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 0.014 0.001 PHE H 154 TYR 0.013 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 114 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.817 Fit side-chains REVERT: A 333 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8619 (m) REVERT: A 353 THR cc_start: 0.8496 (m) cc_final: 0.8259 (p) REVERT: A 412 GLN cc_start: 0.8675 (mm-40) cc_final: 0.7569 (tp-100) REVERT: B 73 ASP cc_start: 0.7978 (t0) cc_final: 0.7272 (t70) REVERT: B 222 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: C 199 GLN cc_start: 0.8837 (tt0) cc_final: 0.8495 (tm-30) REVERT: H 13 GLN cc_start: 0.8795 (mp10) cc_final: 0.8089 (mp10) REVERT: H 87 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7618 (ptp-110) REVERT: L 31 ASN cc_start: 0.8572 (t0) cc_final: 0.7992 (t0) REVERT: L 125 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7187 (mm) REVERT: L 167 ASP cc_start: 0.8488 (t0) cc_final: 0.7893 (t70) outliers start: 29 outliers final: 21 residues processed: 106 average time/residue: 1.0406 time to fit residues: 117.6870 Evaluate side-chains 103 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 58 GLU 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 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 27 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7611 Z= 0.306 Angle : 0.645 9.074 10354 Z= 0.328 Chirality : 0.046 0.154 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.406 53.009 1105 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.47 % Allowed : 19.98 % 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: 0.03 (0.28), residues: 958 helix: -1.30 (0.87), residues: 31 sheet: 0.51 (0.24), residues: 469 loop : -0.31 (0.32), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.002 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.003 0.000 ARG H 105 *********************** 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 fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.897 Fit side-chains REVERT: A 333 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8651 (m) REVERT: A 353 THR cc_start: 0.8532 (m) cc_final: 0.8285 (p) REVERT: A 412 GLN cc_start: 0.8648 (mm-40) cc_final: 0.7525 (tp-100) REVERT: B 73 ASP cc_start: 0.7956 (t0) cc_final: 0.7255 (t70) REVERT: B 222 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: C 199 GLN cc_start: 0.8823 (tt0) cc_final: 0.8474 (tm-30) REVERT: H 13 GLN cc_start: 0.8797 (mp10) cc_final: 0.8094 (mp10) REVERT: H 87 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: L 31 ASN cc_start: 0.8618 (t0) cc_final: 0.8008 (t0) REVERT: L 125 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7107 (mm) REVERT: L 167 ASP cc_start: 0.8516 (t0) cc_final: 0.7931 (t70) outliers start: 29 outliers final: 22 residues processed: 97 average time/residue: 1.0016 time to fit residues: 104.0679 Evaluate side-chains 98 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 58 GLU 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 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 86 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 7611 Z= 0.205 Angle : 0.603 8.280 10354 Z= 0.307 Chirality : 0.045 0.146 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.270 53.618 1105 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.23 % Allowed : 20.45 % 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: 0.13 (0.29), residues: 958 helix: -1.11 (0.91), residues: 31 sheet: 0.57 (0.24), residues: 469 loop : -0.26 (0.32), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 L 142 *********************** 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 107 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.889 Fit side-chains REVERT: A 333 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8593 (m) REVERT: A 353 THR cc_start: 0.8511 (m) cc_final: 0.8296 (p) REVERT: A 412 GLN cc_start: 0.8666 (mm-40) cc_final: 0.7567 (tp-100) REVERT: B 73 ASP cc_start: 0.7994 (t0) cc_final: 0.7321 (t70) REVERT: C 199 GLN cc_start: 0.8841 (tt0) cc_final: 0.8500 (tm-30) REVERT: H 13 GLN cc_start: 0.8790 (mp10) cc_final: 0.8078 (mp10) REVERT: H 87 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7510 (ptp-110) REVERT: L 31 ASN cc_start: 0.8485 (t0) cc_final: 0.7972 (t0) REVERT: L 125 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7208 (mm) REVERT: L 154 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7949 (tt) REVERT: L 167 ASP cc_start: 0.8503 (t0) cc_final: 0.7911 (t70) outliers start: 27 outliers final: 18 residues processed: 98 average time/residue: 0.9998 time to fit residues: 104.9723 Evaluate side-chains 98 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 11 VAL 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 154 LEU 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 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7611 Z= 0.243 Angle : 0.610 7.716 10354 Z= 0.310 Chirality : 0.045 0.139 1191 Planarity : 0.003 0.028 1315 Dihedral : 5.270 53.199 1105 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.75 % Allowed : 20.93 % 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: 0.11 (0.28), residues: 958 helix: -1.07 (0.91), residues: 31 sheet: 0.56 (0.24), residues: 469 loop : -0.27 (0.32), residues: 458 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 0.014 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.004 0.000 ARG L 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.882 Fit side-chains REVERT: A 333 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8612 (m) REVERT: A 353 THR cc_start: 0.8453 (m) cc_final: 0.8237 (p) REVERT: A 412 GLN cc_start: 0.8654 (mm-40) cc_final: 0.7539 (tp-100) REVERT: B 73 ASP cc_start: 0.7994 (t0) cc_final: 0.7295 (t70) REVERT: C 199 GLN cc_start: 0.8833 (tt0) cc_final: 0.8491 (tm-30) REVERT: H 13 GLN cc_start: 0.8835 (mp10) cc_final: 0.8108 (mp10) REVERT: L 31 ASN cc_start: 0.8512 (t0) cc_final: 0.7990 (t0) REVERT: L 123 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7444 (mp0) REVERT: L 125 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7160 (mm) REVERT: L 154 LEU cc_start: 0.8258 (mm) cc_final: 0.7968 (tt) REVERT: L 167 ASP cc_start: 0.8511 (t0) cc_final: 0.7920 (t70) outliers start: 23 outliers final: 18 residues processed: 96 average time/residue: 1.0827 time to fit residues: 111.0301 Evaluate side-chains 94 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 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 103 ASP Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain H residue 11 VAL 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 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 53 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 = 0.3534 r_free = 0.3534 target = 0.089373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.075072 restraints weight = 17156.313| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.80 r_work: 0.3153 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7611 Z= 0.283 Angle : 0.629 8.109 10354 Z= 0.321 Chirality : 0.046 0.145 1191 Planarity : 0.003 0.029 1315 Dihedral : 5.364 53.127 1105 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.87 % Allowed : 21.29 % 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: 0.05 (0.28), residues: 958 helix: -1.11 (0.90), residues: 31 sheet: 0.53 (0.24), residues: 469 loop : -0.32 (0.32), residues: 458 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 0.016 0.002 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.004 0.000 ARG L 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.07 seconds wall clock time: 50 minutes 45.97 seconds (3045.97 seconds total)