Starting phenix.real_space_refine on Tue Jun 25 09:05:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/06_2024/8r9z_19017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/06_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_19017/06_2024/8r9z_19017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/06_2024/8r9z_19017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/06_2024/8r9z_19017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9z_19017/06_2024/8r9z_19017.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 4.98, per 1000 atoms: 0.67 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: 2.98 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: 1.01 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: 3.27 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 2.440 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.277 2.440 nonbonded pdb=" O ASP C 82 " pdb=" OH TYR C 86 " model vdw 2.300 2.440 nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.307 2.440 nonbonded pdb=" OE1 GLN B 62 " pdb=" NH1 ARG B 65 " model vdw 2.310 2.520 ... (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 ========== 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: 1.850 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: 6.110 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.520 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.070 ------------------------------------------------------------------------------- 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: 1.4080 time to fit residues: 185.7835 Evaluate side-chains 88 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- 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: 0.8630 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7606 Z= 0.357 Angle : 0.670 9.496 10347 Z= 0.351 Chirality : 0.047 0.182 1191 Planarity : 0.004 0.034 1314 Dihedral : 5.391 51.470 1104 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.80 % Allowed : 9.58 % Favored : 88.62 % 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: 0.23 (0.29), residues: 958 helix: -1.84 (0.82), residues: 31 sheet: 0.57 (0.24), residues: 467 loop : -0.02 (0.33), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 94 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.002 PHE H 154 TYR 0.013 0.001 TYR L 140 ARG 0.006 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9063 (mm110) cc_final: 0.8824 (mm110) REVERT: B 222 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: C 18 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8187 (ttm110) REVERT: H 89 GLU cc_start: 0.8412 (pm20) cc_final: 0.8138 (pm20) REVERT: L 4 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.9082 (mmm) REVERT: L 17 ASP cc_start: 0.8277 (m-30) cc_final: 0.8010 (m-30) REVERT: L 142 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.8066 (tmt90) REVERT: L 165 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8424 (mm-30) outliers start: 15 outliers final: 5 residues processed: 88 average time/residue: 1.3730 time to fit residues: 127.1597 Evaluate side-chains 84 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 103 ASP 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 C residue 185 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 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 A 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1725 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= 0.284 Angle : 0.623 8.488 10347 Z= 0.325 Chirality : 0.045 0.182 1191 Planarity : 0.004 0.035 1314 Dihedral : 5.314 51.381 1104 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.16 % Allowed : 12.57 % Favored : 85.27 % 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: -1.60 (0.86), residues: 31 sheet: 0.58 (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 0.003 0.001 HIS C 198 PHE 0.013 0.001 PHE H 154 TYR 0.013 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 98 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9062 (mm110) cc_final: 0.8836 (mm110) REVERT: B 207 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8190 (m-40) REVERT: B 222 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: C 18 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8228 (ttm110) REVERT: H 89 GLU cc_start: 0.8405 (pm20) cc_final: 0.8118 (pm20) REVERT: L 4 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8860 (mmm) REVERT: L 17 ASP cc_start: 0.8276 (m-30) cc_final: 0.8002 (m-30) REVERT: L 142 ARG cc_start: 0.8432 (ttt-90) cc_final: 0.8186 (tmt90) REVERT: L 145 LYS cc_start: 0.7994 (pttt) cc_final: 0.7759 (ptmm) REVERT: L 187 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8262 (mm-30) outliers start: 18 outliers final: 6 residues processed: 89 average time/residue: 1.3852 time to fit residues: 129.8480 Evaluate side-chains 84 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU 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 207 ASN Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 185 ASP 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: 2.9990 chunk 64 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 0.051 7606 Z= 0.330 Angle : 0.642 8.630 10347 Z= 0.333 Chirality : 0.046 0.187 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.381 50.633 1104 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.99 % Allowed : 13.65 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.65 (0.83), residues: 31 sheet: 0.53 (0.24), residues: 466 loop : -0.06 (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 0.013 0.001 PHE H 154 TYR 0.014 0.001 TYR L 140 ARG 0.010 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 105 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8900 (m-80) cc_final: 0.8694 (m-80) REVERT: B 43 GLN cc_start: 0.9067 (mm110) cc_final: 0.8849 (mm110) REVERT: B 65 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8670 (mtt-85) REVERT: B 222 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: H 89 GLU cc_start: 0.8367 (pm20) cc_final: 0.8088 (pm20) REVERT: L 4 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8848 (mmm) REVERT: L 17 ASP cc_start: 0.8266 (m-30) cc_final: 0.7978 (m-30) REVERT: L 24 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7932 (mtp-110) REVERT: L 187 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8264 (mm-30) outliers start: 25 outliers final: 11 residues processed: 93 average time/residue: 1.4338 time to fit residues: 140.4254 Evaluate side-chains 90 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 THR 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 C residue 185 ASP Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7606 Z= 0.234 Angle : 0.598 7.740 10347 Z= 0.310 Chirality : 0.045 0.183 1191 Planarity : 0.004 0.035 1314 Dihedral : 5.269 51.425 1104 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.63 % Allowed : 15.57 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 958 helix: -1.55 (0.85), residues: 31 sheet: 0.61 (0.24), residues: 460 loop : -0.04 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 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 H 16 *********************** 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 105 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8920 (m-80) cc_final: 0.8715 (m-80) REVERT: B 43 GLN cc_start: 0.9035 (mm110) cc_final: 0.8810 (mm110) REVERT: B 65 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8580 (mtt-85) REVERT: B 207 ASN cc_start: 0.8385 (m-40) cc_final: 0.8166 (m-40) REVERT: B 222 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: H 89 GLU cc_start: 0.8363 (pm20) cc_final: 0.8081 (pm20) REVERT: L 4 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8846 (mmm) REVERT: L 17 ASP cc_start: 0.8278 (m-30) cc_final: 0.8014 (m-30) REVERT: L 24 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7889 (mtp-110) REVERT: L 142 ARG cc_start: 0.8220 (tpt-90) cc_final: 0.7990 (tmt-80) REVERT: L 187 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8289 (mm-30) outliers start: 22 outliers final: 12 residues processed: 95 average time/residue: 1.2274 time to fit residues: 123.2055 Evaluate side-chains 92 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 THR 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 30 ASN 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 L residue 1 ASP Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8657 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7606 Z= 0.387 Angle : 0.668 10.050 10347 Z= 0.347 Chirality : 0.047 0.192 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.474 49.779 1104 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.71 % Allowed : 16.05 % 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: -1.65 (0.83), residues: 31 sheet: 0.54 (0.24), residues: 465 loop : -0.07 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 94 HIS 0.004 0.001 HIS B 174 PHE 0.015 0.002 PHE H 154 TYR 0.018 0.002 TYR B 80 ARG 0.005 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 106 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8924 (m-80) cc_final: 0.8722 (m-80) REVERT: B 43 GLN cc_start: 0.9071 (mm110) cc_final: 0.8827 (mm110) REVERT: B 65 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8709 (mtt-85) REVERT: H 89 GLU cc_start: 0.8403 (pm20) cc_final: 0.8119 (pm20) REVERT: L 4 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8869 (mmm) REVERT: L 17 ASP cc_start: 0.8265 (m-30) cc_final: 0.7991 (m-30) REVERT: L 24 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7875 (mtp-110) REVERT: L 165 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: L 187 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8209 (mm-30) outliers start: 31 outliers final: 15 residues processed: 95 average time/residue: 1.3034 time to fit residues: 130.7215 Evaluate side-chains 90 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 1 ASP 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: 2.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 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 0.045 7606 Z= 0.253 Angle : 0.618 9.182 10347 Z= 0.321 Chirality : 0.045 0.186 1191 Planarity : 0.004 0.035 1314 Dihedral : 5.362 51.188 1104 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.63 % Allowed : 17.60 % Favored : 79.76 % 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: 0.26 (0.28), residues: 958 helix: -1.61 (0.82), residues: 31 sheet: 0.61 (0.24), residues: 458 loop : -0.04 (0.32), residues: 469 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 0.014 0.001 PHE H 154 TYR 0.021 0.001 TYR A 334 ARG 0.007 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 104 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9041 (mm110) cc_final: 0.8830 (mm110) REVERT: B 65 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8626 (mtt-85) REVERT: B 207 ASN cc_start: 0.8391 (m-40) cc_final: 0.8164 (m-40) REVERT: H 89 GLU cc_start: 0.8395 (pm20) cc_final: 0.8115 (pm20) REVERT: L 4 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8889 (mmm) REVERT: L 17 ASP cc_start: 0.8275 (m-30) cc_final: 0.7998 (m-30) REVERT: L 24 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7942 (mtp-110) REVERT: L 165 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: L 187 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8228 (mm-30) outliers start: 22 outliers final: 11 residues processed: 96 average time/residue: 1.3241 time to fit residues: 133.9929 Evaluate side-chains 88 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 THR 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 185 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 152 ASN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7606 Z= 0.305 Angle : 0.644 9.096 10347 Z= 0.334 Chirality : 0.046 0.189 1191 Planarity : 0.004 0.035 1314 Dihedral : 5.389 50.875 1104 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.47 % Allowed : 17.25 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 958 helix: -1.62 (0.81), residues: 31 sheet: 0.54 (0.24), residues: 461 loop : -0.09 (0.32), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 94 HIS 0.004 0.001 HIS C 198 PHE 0.013 0.001 PHE H 154 TYR 0.022 0.002 TYR A 334 ARG 0.008 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 104 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 75 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9071 (mm110) cc_final: 0.8850 (mm110) REVERT: B 65 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8682 (mtt-85) REVERT: H 89 GLU cc_start: 0.8387 (pm20) cc_final: 0.8121 (pm20) REVERT: H 220 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: L 4 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8888 (mmm) REVERT: L 17 ASP cc_start: 0.8276 (m-30) cc_final: 0.8014 (m-30) REVERT: L 24 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7933 (mtp-110) REVERT: L 165 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8447 (mm-30) REVERT: L 187 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8245 (mm-30) outliers start: 29 outliers final: 18 residues processed: 95 average time/residue: 1.2356 time to fit residues: 124.2291 Evaluate side-chains 95 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 175 THR 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 30 ASN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP 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 220 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN L 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7606 Z= 0.229 Angle : 0.617 8.595 10347 Z= 0.320 Chirality : 0.045 0.185 1191 Planarity : 0.004 0.035 1314 Dihedral : 5.289 51.677 1104 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.75 % Allowed : 18.56 % Favored : 78.68 % 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: 0.28 (0.28), residues: 958 helix: -1.42 (0.86), residues: 30 sheet: 0.59 (0.24), residues: 469 loop : -0.02 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 PHE 0.012 0.001 PHE H 154 TYR 0.023 0.001 TYR A 334 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 105 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9032 (mm110) cc_final: 0.8819 (mm110) REVERT: B 65 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8654 (mtt-85) REVERT: B 207 ASN cc_start: 0.8350 (m-40) cc_final: 0.8125 (m-40) REVERT: H 89 GLU cc_start: 0.8400 (pm20) cc_final: 0.8132 (pm20) REVERT: L 4 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8911 (mmm) REVERT: L 17 ASP cc_start: 0.8290 (m-30) cc_final: 0.8023 (m-30) REVERT: L 24 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7925 (mtp-110) REVERT: L 165 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: L 187 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8271 (mm-30) outliers start: 23 outliers final: 14 residues processed: 97 average time/residue: 1.2115 time to fit residues: 124.4021 Evaluate side-chains 94 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 65 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8640 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7606 Z= 0.317 Angle : 0.655 8.975 10347 Z= 0.340 Chirality : 0.046 0.191 1191 Planarity : 0.004 0.036 1314 Dihedral : 5.370 50.858 1104 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.51 % Allowed : 19.28 % Favored : 78.20 % 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: 0.20 (0.28), residues: 958 helix: -1.61 (0.81), residues: 31 sheet: 0.54 (0.24), residues: 468 loop : -0.06 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 94 HIS 0.004 0.001 HIS C 198 PHE 0.013 0.001 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 97 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 43 GLN cc_start: 0.9063 (mm110) cc_final: 0.8838 (mm110) REVERT: H 89 GLU cc_start: 0.8412 (pm20) cc_final: 0.8150 (pm20) REVERT: L 4 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.8886 (mmm) REVERT: L 17 ASP cc_start: 0.8285 (m-30) cc_final: 0.8020 (m-30) REVERT: L 24 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7924 (mtp-110) REVERT: L 165 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8423 (mm-30) REVERT: L 187 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8274 (mm-30) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 1.2636 time to fit residues: 118.9063 Evaluate side-chains 89 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067980 restraints weight = 17976.016| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.91 r_work: 0.2987 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7606 Z= 0.200 Angle : 0.611 8.346 10347 Z= 0.316 Chirality : 0.045 0.184 1191 Planarity : 0.004 0.034 1314 Dihedral : 5.233 52.132 1104 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.28 % Allowed : 19.28 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 958 helix: -1.42 (0.85), residues: 31 sheet: 0.58 (0.24), residues: 469 loop : 0.03 (0.33), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 164 HIS 0.003 0.001 HIS C 198 PHE 0.011 0.001 PHE H 154 TYR 0.027 0.001 TYR A 334 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: 2856.11 seconds wall clock time: 51 minutes 15.39 seconds (3075.39 seconds total)