Starting phenix.real_space_refine on Sat Aug 3 07:40:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/08_2024/8r9z_19017.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/08_2024/8r9z_19017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/08_2024/8r9z_19017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/08_2024/8r9z_19017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/08_2024/8r9z_19017.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/08_2024/8r9z_19017.cif" } resolution = 2.9 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4682 2.51 5 N 1246 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7441 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1614 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain breaks: 1 Chain: "C" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 197} Chain: "H" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1654 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.09, per 1000 atoms: 0.68 Number of scatterers: 7441 At special positions: 0 Unit cell: (73.9731, 105.12, 145.026, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1478 8.00 N 1246 7.00 C 4682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.05 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.87 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 24 sheets defined 6.4% alpha, 49.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.801A pdb=" N ASN A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.707A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.700A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.634A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'H' and resid 195 through 198 removed outlier: 4.319A pdb=" N GLY H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 195 through 198' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.687A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.523A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.154A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 removed outlier: 8.393A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 11.233A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 11.798A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 316 removed outlier: 6.870A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.581A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 57 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.641A pdb=" N ILE B 112 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 134 removed outlier: 3.549A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 190 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 130 through 134 removed outlier: 3.549A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 190 " --> pdb=" O CYS B 150 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.119A pdb=" N GLU C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.631A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.849A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.355A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.649A pdb=" N CYS C 194 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.653A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.640A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB9, first strand: chain 'H' and resid 129 through 131 removed outlier: 5.781A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AC2, first strand: chain 'H' and resid 158 through 162 removed outlier: 4.604A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.832A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.657A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.705A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 145 through 150 removed outlier: 4.309A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR L 197 " --> pdb=" O LYS L 145 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2374 1.35 - 1.47: 2001 1.47 - 1.60: 3183 1.60 - 1.72: 0 1.72 - 1.85: 48 Bond restraints: 7606 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" CB CYS A 335 " pdb=" SG CYS A 335 " ideal model delta sigma weight residual 1.808 1.850 -0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 ... (remaining 7601 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.62: 235 106.62 - 113.46: 4229 113.46 - 120.30: 2445 120.30 - 127.14: 3341 127.14 - 133.98: 97 Bond angle restraints: 10347 Sorted by residual: angle pdb=" CA CYS A 378 " pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " ideal model delta sigma weight residual 114.40 122.57 -8.17 2.30e+00 1.89e-01 1.26e+01 angle pdb=" CA LEU B 200 " pdb=" CB LEU B 200 " pdb=" CG LEU B 200 " ideal model delta sigma weight residual 116.30 128.31 -12.01 3.50e+00 8.16e-02 1.18e+01 angle pdb=" N VAL L 150 " pdb=" CA VAL L 150 " pdb=" C VAL L 150 " ideal model delta sigma weight residual 106.21 109.65 -3.44 1.07e+00 8.73e-01 1.03e+01 angle pdb=" C VAL L 150 " pdb=" N ASP L 151 " pdb=" CA ASP L 151 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" C LYS H 151 " pdb=" N ASP H 152 " pdb=" CA ASP H 152 " ideal model delta sigma weight residual 121.26 125.93 -4.67 1.59e+00 3.96e-01 8.64e+00 ... (remaining 10342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 4181 16.79 - 33.58: 322 33.58 - 50.36: 63 50.36 - 67.15: 18 67.15 - 83.94: 11 Dihedral angle restraints: 4595 sinusoidal: 1790 harmonic: 2805 Sorted by residual: dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual 93.00 153.27 -60.27 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS A 335 " pdb=" SG CYS A 335 " pdb=" SG CYS A 378 " pdb=" CB CYS A 378 " ideal model delta sinusoidal sigma weight residual 93.00 47.21 45.79 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 206 " pdb=" CB CYS B 206 " ideal model delta sinusoidal sigma weight residual 93.00 138.25 -45.25 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 4592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 852 0.040 - 0.080: 211 0.080 - 0.120: 115 0.120 - 0.160: 12 0.160 - 0.200: 1 Chirality restraints: 1191 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 52 " pdb=" N ILE B 52 " pdb=" C ILE B 52 " pdb=" CB ILE B 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1188 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 194 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 195 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO L 80 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 166 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C GLN C 166 " -0.021 2.00e-02 2.50e+03 pdb=" O GLN C 166 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP C 167 " 0.007 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1929 2.80 - 3.33: 6285 3.33 - 3.85: 11995 3.85 - 4.38: 14282 4.38 - 4.90: 25642 Nonbonded interactions: 60133 Sorted by model distance: nonbonded pdb=" OG SER C 121 " pdb=" OE1 GLU C 123 " model vdw 2.276 3.040 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.277 3.040 nonbonded pdb=" O ASP C 82 " pdb=" OH TYR C 86 " model vdw 2.300 3.040 nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLN B 62 " pdb=" NH1 ARG B 65 " model vdw 2.310 3.120 ... (remaining 60128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7606 Z= 0.190 Angle : 0.568 12.009 10347 Z= 0.290 Chirality : 0.044 0.200 1191 Planarity : 0.004 0.044 1314 Dihedral : 13.351 83.940 2762 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.81), residues: 30 sheet: 0.45 (0.25), residues: 463 loop : 0.00 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 94 HIS 0.003 0.001 HIS C 198 PHE 0.008 0.001 PHE L 71 TYR 0.012 0.001 TYR L 140 ARG 0.001 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ASN cc_start: 0.8692 (m-40) cc_final: 0.8467 (p0) REVERT: B 43 GLN cc_start: 0.8994 (mm110) cc_final: 0.8781 (mm110) REVERT: H 12 VAL cc_start: 0.9025 (p) cc_final: 0.8761 (m) REVERT: H 89 GLU cc_start: 0.8450 (pm20) cc_final: 0.8175 (pm20) REVERT: L 17 ASP cc_start: 0.8309 (m-30) cc_final: 0.8089 (m-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.4709 time to fit residues: 193.9014 Evaluate side-chains 88 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7606 Z= 0.370 Angle : 0.693 9.485 10347 Z= 0.363 Chirality : 0.048 0.184 1191 Planarity : 0.005 0.036 1314 Dihedral : 5.436 50.569 1104 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.56 % Allowed : 10.06 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 958 helix: -1.70 (0.86), residues: 31 sheet: 0.52 (0.24), residues: 467 loop : -0.04 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.004 0.001 HIS B 174 PHE 0.014 0.002 PHE B 156 TYR 0.014 0.001 TYR L 140 ARG 0.006 0.001 ARG L 142 *********************** 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 100 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9076 (mm110) cc_final: 0.8837 (mm110) REVERT: B 222 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: C 18 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8163 (ttm110) REVERT: H 89 GLU cc_start: 0.8636 (pm20) cc_final: 0.8276 (pm20) REVERT: H 103 MET cc_start: 0.8979 (mtt) cc_final: 0.8557 (mtt) REVERT: L 4 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9030 (mmm) REVERT: L 17 ASP cc_start: 0.8261 (m-30) cc_final: 0.8029 (m-30) REVERT: L 142 ARG cc_start: 0.8383 (ttt-90) cc_final: 0.8067 (tmt90) outliers start: 13 outliers final: 3 residues processed: 92 average time/residue: 1.4976 time to fit residues: 144.6305 Evaluate side-chains 82 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 122 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 68 optimal weight: 6.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7606 Z= 0.263 Angle : 0.629 8.475 10347 Z= 0.329 Chirality : 0.046 0.182 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.331 50.763 1104 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.56 % Allowed : 13.77 % Favored : 84.67 % 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: 0.26 (0.29), residues: 958 helix: -1.47 (0.87), residues: 31 sheet: 0.55 (0.24), residues: 466 loop : 0.01 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 94 HIS 0.003 0.001 HIS C 198 PHE 0.012 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.006 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 95 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9057 (mm110) cc_final: 0.8837 (mm110) REVERT: B 207 ASN cc_start: 0.8391 (m-40) cc_final: 0.8171 (m-40) REVERT: B 222 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: C 18 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8230 (ttm110) REVERT: H 89 GLU cc_start: 0.8616 (pm20) cc_final: 0.8243 (pm20) REVERT: L 4 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8884 (mmm) REVERT: L 17 ASP cc_start: 0.8273 (m-30) cc_final: 0.8048 (m-30) REVERT: L 142 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.8206 (tmt90) REVERT: L 145 LYS cc_start: 0.8029 (pttt) cc_final: 0.7787 (ptmm) REVERT: L 187 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8299 (mm-30) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 1.3301 time to fit residues: 126.2712 Evaluate side-chains 84 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7606 Z= 0.315 Angle : 0.638 8.233 10347 Z= 0.333 Chirality : 0.046 0.185 1191 Planarity : 0.004 0.043 1314 Dihedral : 5.370 50.326 1104 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.63 % Allowed : 13.77 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 958 helix: -1.52 (0.85), residues: 31 sheet: 0.50 (0.24), residues: 466 loop : -0.02 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 94 HIS 0.004 0.001 HIS C 198 PHE 0.013 0.001 PHE H 154 TYR 0.016 0.001 TYR A 334 ARG 0.009 0.001 ARG L 24 *********************** 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 101 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9057 (mm110) cc_final: 0.8826 (mm110) REVERT: B 222 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: H 89 GLU cc_start: 0.8602 (pm20) cc_final: 0.8303 (pm20) REVERT: L 4 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8881 (mmm) REVERT: L 17 ASP cc_start: 0.8255 (m-30) cc_final: 0.8046 (m-30) REVERT: L 24 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7935 (mtp-110) REVERT: L 142 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8258 (tmt90) REVERT: L 165 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: L 187 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8316 (mm-30) outliers start: 22 outliers final: 7 residues processed: 93 average time/residue: 1.3864 time to fit residues: 135.6650 Evaluate side-chains 86 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7606 Z= 0.236 Angle : 0.614 7.704 10347 Z= 0.320 Chirality : 0.045 0.184 1191 Planarity : 0.004 0.033 1314 Dihedral : 5.281 50.834 1104 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.80 % Allowed : 15.69 % Favored : 82.51 % 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: 0.26 (0.28), residues: 958 helix: -1.47 (0.86), residues: 31 sheet: 0.55 (0.24), residues: 460 loop : 0.01 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 PHE 0.011 0.001 PHE H 154 TYR 0.014 0.001 TYR L 140 ARG 0.007 0.001 ARG C 54 *********************** 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 100 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9046 (mm110) cc_final: 0.8820 (mm110) REVERT: B 207 ASN cc_start: 0.8374 (m-40) cc_final: 0.8129 (m-40) REVERT: H 89 GLU cc_start: 0.8585 (pm20) cc_final: 0.8250 (pm20) REVERT: L 4 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.8887 (mmm) REVERT: L 24 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7884 (mtp-110) REVERT: L 165 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8404 (mm-30) REVERT: L 187 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8281 (mm-30) outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 1.2954 time to fit residues: 130.9528 Evaluate side-chains 86 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7606 Z= 0.286 Angle : 0.635 9.804 10347 Z= 0.330 Chirality : 0.046 0.186 1191 Planarity : 0.004 0.034 1314 Dihedral : 5.311 50.536 1104 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.99 % Allowed : 15.81 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 958 helix: -1.46 (0.86), residues: 31 sheet: 0.53 (0.24), residues: 464 loop : 0.00 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 94 HIS 0.003 0.001 HIS C 198 PHE 0.013 0.001 PHE H 154 TYR 0.019 0.001 TYR A 334 ARG 0.006 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9058 (mm110) cc_final: 0.8820 (mm110) REVERT: B 207 ASN cc_start: 0.8352 (m-40) cc_final: 0.8102 (m-40) REVERT: H 89 GLU cc_start: 0.8579 (pm20) cc_final: 0.8190 (pm20) REVERT: L 4 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: L 24 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7882 (mtp-110) REVERT: L 165 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8399 (mm-30) REVERT: L 187 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8304 (mm-30) outliers start: 25 outliers final: 10 residues processed: 97 average time/residue: 1.2932 time to fit residues: 132.5620 Evaluate side-chains 86 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 165 GLU 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: 2.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7606 Z= 0.225 Angle : 0.619 8.752 10347 Z= 0.322 Chirality : 0.045 0.186 1191 Planarity : 0.004 0.037 1314 Dihedral : 5.265 51.164 1104 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.16 % Allowed : 16.65 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 958 helix: -1.37 (0.86), residues: 31 sheet: 0.59 (0.24), residues: 464 loop : 0.06 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 PHE 0.011 0.001 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.008 0.001 ARG C 54 *********************** 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 99 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9046 (mm110) cc_final: 0.8821 (mm110) REVERT: B 207 ASN cc_start: 0.8386 (m-40) cc_final: 0.8125 (m-40) REVERT: H 89 GLU cc_start: 0.8566 (pm20) cc_final: 0.8178 (pm20) REVERT: L 4 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8891 (mmm) REVERT: L 24 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7825 (mtp-110) REVERT: L 165 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: L 187 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8270 (mm-30) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 1.2267 time to fit residues: 122.0618 Evaluate side-chains 87 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7606 Z= 0.382 Angle : 0.685 9.086 10347 Z= 0.357 Chirality : 0.047 0.194 1191 Planarity : 0.004 0.035 1314 Dihedral : 5.486 49.954 1104 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.40 % Allowed : 17.25 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 958 helix: -1.43 (0.86), residues: 31 sheet: 0.47 (0.24), residues: 464 loop : -0.14 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.004 0.001 HIS C 198 PHE 0.015 0.002 PHE H 154 TYR 0.027 0.002 TYR A 334 ARG 0.009 0.001 ARG H 16 *********************** 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 95 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9069 (mm110) cc_final: 0.8844 (mm110) REVERT: H 89 GLU cc_start: 0.8570 (pm20) cc_final: 0.8189 (pm20) REVERT: L 4 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8918 (mmm) REVERT: L 24 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7916 (mtp-110) REVERT: L 187 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8313 (mm-30) outliers start: 20 outliers final: 12 residues processed: 89 average time/residue: 1.3364 time to fit residues: 125.6982 Evaluate side-chains 83 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7606 Z= 0.249 Angle : 0.642 8.808 10347 Z= 0.335 Chirality : 0.046 0.188 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.361 51.068 1104 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.80 % Allowed : 17.96 % Favored : 80.24 % 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: 0.18 (0.28), residues: 958 helix: -1.30 (0.86), residues: 31 sheet: 0.55 (0.24), residues: 465 loop : -0.13 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 113 HIS 0.003 0.001 HIS C 198 PHE 0.013 0.001 PHE H 154 TYR 0.014 0.001 TYR L 140 ARG 0.008 0.001 ARG C 54 *********************** 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 93 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9041 (mm110) cc_final: 0.8840 (mm110) REVERT: H 89 GLU cc_start: 0.8546 (pm20) cc_final: 0.8172 (pm20) REVERT: L 4 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8923 (mmm) REVERT: L 24 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7911 (mtp-110) REVERT: L 187 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8347 (mm-30) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 1.3348 time to fit residues: 125.4028 Evaluate side-chains 86 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS 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: 0.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7606 Z= 0.387 Angle : 0.699 9.136 10347 Z= 0.365 Chirality : 0.047 0.198 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.516 50.143 1104 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.04 % Allowed : 18.08 % Favored : 79.88 % 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: 0.07 (0.28), residues: 958 helix: -1.39 (0.84), residues: 31 sheet: 0.49 (0.24), residues: 465 loop : -0.22 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 113 HIS 0.004 0.001 HIS C 198 PHE 0.015 0.002 PHE H 154 TYR 0.026 0.002 TYR A 334 ARG 0.008 0.001 ARG C 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9087 (mm110) cc_final: 0.8871 (mm110) REVERT: H 89 GLU cc_start: 0.8567 (pm20) cc_final: 0.8219 (pm20) REVERT: L 4 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8908 (mmm) REVERT: L 24 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7937 (mtp-110) REVERT: L 187 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8296 (mm-30) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 1.2722 time to fit residues: 117.0402 Evaluate side-chains 84 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 53 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067735 restraints weight = 17874.727| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.91 r_work: 0.2982 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7606 Z= 0.187 Angle : 0.635 8.477 10347 Z= 0.331 Chirality : 0.045 0.185 1191 Planarity : 0.004 0.037 1314 Dihedral : 5.329 51.734 1104 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.80 % Allowed : 18.20 % Favored : 80.00 % 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: 0.18 (0.28), residues: 958 helix: -1.24 (0.85), residues: 31 sheet: 0.55 (0.24), residues: 467 loop : -0.13 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 PHE 0.012 0.001 PHE H 154 TYR 0.015 0.001 TYR B 80 ARG 0.009 0.001 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.45 seconds wall clock time: 51 minutes 45.22 seconds (3105.22 seconds total)