Starting phenix.real_space_refine on Sat Aug 3 14:35:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xql_38580/08_2024/8xql_38580.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xql_38580/08_2024/8xql_38580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xql_38580/08_2024/8xql_38580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xql_38580/08_2024/8xql_38580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xql_38580/08_2024/8xql_38580.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xql_38580/08_2024/8xql_38580.cif" } resolution = 2.99 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= 0.001 sd= 0.021 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 48 5.16 5 C 5342 2.51 5 N 1439 2.21 5 O 1539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1964 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 981 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2293 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Chain breaks: 1 Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'CLR': 1, 'GOQ': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.32, per 1000 atoms: 0.64 Number of scatterers: 8368 At special positions: 0 Unit cell: (75.92, 99.84, 133.12, 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 48 16.00 O 1539 8.00 N 1439 7.00 C 5342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 100 " - pdb=" SG CYS N 108 " distance=2.02 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 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 45.2% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.804A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 135 through 138 removed outlier: 3.728A pdb=" N ARG A 138 " --> pdb=" O ARG A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.529A pdb=" N ALA A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.529A pdb=" N TYR A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 222 through 246 removed outlier: 3.781A pdb=" N ASN A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.508A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.643A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.570A pdb=" N ASN N 32 " --> pdb=" O THR N 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR N 33 " --> pdb=" O PHE N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 33' Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 3 through 37 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 74 through 78 Processing helix chain 'R' and resid 80 through 112 Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.646A pdb=" N TRP R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 158 removed outlier: 4.591A pdb=" N VAL R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 216 Proline residue: R 190 - end of helix Processing helix chain 'R' and resid 220 through 254 Processing helix chain 'R' and resid 260 through 284 removed outlier: 3.822A pdb=" N LEU R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.914A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 79 removed outlier: 6.120A pdb=" N HIS A 37 " --> pdb=" O HIS A 85 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 87 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 39 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.491A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.867A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.058A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.862A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.292A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.410A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.448A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1374 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: 2.50 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2687 1.34 - 1.46: 1477 1.46 - 1.57: 4312 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 8545 Sorted by residual: bond pdb=" C8 GOQ R 502 " pdb=" C9 GOQ R 502 " ideal model delta sigma weight residual 1.350 1.388 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C5 GOQ R 502 " pdb=" C6 GOQ R 502 " ideal model delta sigma weight residual 1.454 1.417 0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C5 GOQ R 501 " pdb=" C6 GOQ R 501 " ideal model delta sigma weight residual 1.454 1.420 0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" C8 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.350 1.383 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C10 GOQ R 501 " pdb=" C9 GOQ R 501 " ideal model delta sigma weight residual 1.423 1.392 0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 8540 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.39: 97 105.39 - 112.54: 4491 112.54 - 119.69: 2737 119.69 - 126.83: 4136 126.83 - 133.98: 111 Bond angle restraints: 11572 Sorted by residual: angle pdb=" CA VAL N 127 " pdb=" CB VAL N 127 " pdb=" CG1 VAL N 127 " ideal model delta sigma weight residual 110.40 115.55 -5.15 1.70e+00 3.46e-01 9.19e+00 angle pdb=" C CYS N 100 " pdb=" CA CYS N 100 " pdb=" CB CYS N 100 " ideal model delta sigma weight residual 109.11 113.50 -4.39 1.50e+00 4.44e-01 8.57e+00 angle pdb=" CA LEU A 157 " pdb=" CB LEU A 157 " pdb=" CG LEU A 157 " ideal model delta sigma weight residual 116.30 126.30 -10.00 3.50e+00 8.16e-02 8.17e+00 angle pdb=" N PRO N 101 " pdb=" CA PRO N 101 " pdb=" C PRO N 101 " ideal model delta sigma weight residual 112.47 118.21 -5.74 2.06e+00 2.36e-01 7.77e+00 angle pdb=" C PHE R 72 " pdb=" CA PHE R 72 " pdb=" CB PHE R 72 " ideal model delta sigma weight residual 110.17 115.58 -5.41 1.97e+00 2.58e-01 7.54e+00 ... (remaining 11567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4469 17.86 - 35.71: 487 35.71 - 53.57: 120 53.57 - 71.42: 11 71.42 - 89.28: 7 Dihedral angle restraints: 5094 sinusoidal: 2052 harmonic: 3042 Sorted by residual: dihedral pdb=" CA CYS N 100 " pdb=" C CYS N 100 " pdb=" N PRO N 101 " pdb=" CA PRO N 101 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 97 " pdb=" CB CYS N 97 " ideal model delta sinusoidal sigma weight residual 93.00 57.60 35.40 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA CYS N 108 " pdb=" C CYS N 108 " pdb=" N PHE N 109 " pdb=" CA PHE N 109 " ideal model delta harmonic sigma weight residual 180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 5091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 817 0.034 - 0.068: 342 0.068 - 0.101: 103 0.101 - 0.135: 38 0.135 - 0.169: 7 Chirality restraints: 1307 Sorted by residual: chirality pdb=" CA PRO N 101 " pdb=" N PRO N 101 " pdb=" C PRO N 101 " pdb=" CB PRO N 101 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB ILE R 19 " pdb=" CA ILE R 19 " pdb=" CG1 ILE R 19 " pdb=" CG2 ILE R 19 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE R 242 " pdb=" CA ILE R 242 " pdb=" CG1 ILE R 242 " pdb=" CG2 ILE R 242 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1304 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 87 " -0.006 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE A 87 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 87 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 87 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 87 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 87 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 87 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO C 49 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" CG ASN A 134 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.008 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 297 2.70 - 3.25: 8606 3.25 - 3.80: 14406 3.80 - 4.35: 17832 4.35 - 4.90: 29868 Nonbonded interactions: 71009 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASN R 24 " pdb=" OG SER R 277 " model vdw 2.188 3.040 nonbonded pdb=" O ALA A 44 " pdb=" OG SER A 47 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.221 3.040 ... (remaining 71004 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=1.00 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.160 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.005 0.057 8545 Z= 0.329 Angle : 0.628 10.001 11572 Z= 0.330 Chirality : 0.044 0.169 1307 Planarity : 0.004 0.038 1450 Dihedral : 15.562 89.276 3118 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 26.71 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.26), residues: 1038 helix: 2.36 (0.24), residues: 440 sheet: -0.24 (0.35), residues: 218 loop : -0.85 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 151 PHE 0.023 0.002 PHE A 87 TYR 0.016 0.002 TYR N 96 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 ASN cc_start: 0.8143 (m-40) cc_final: 0.7912 (m110) REVERT: B 186 ASP cc_start: 0.7639 (m-30) cc_final: 0.7428 (m-30) REVERT: B 226 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7636 (mt-10) outliers start: 0 outliers final: 1 residues processed: 224 average time/residue: 1.1640 time to fit residues: 277.2573 Evaluate side-chains 220 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 155 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8545 Z= 0.266 Angle : 0.570 7.921 11572 Z= 0.301 Chirality : 0.042 0.179 1307 Planarity : 0.004 0.049 1450 Dihedral : 4.474 34.211 1213 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 4.64 % Allowed : 22.30 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.26), residues: 1038 helix: 2.53 (0.23), residues: 440 sheet: -0.05 (0.36), residues: 210 loop : -0.83 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS A 212 PHE 0.019 0.002 PHE A 87 TYR 0.014 0.001 TYR N 96 ARG 0.005 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: A 134 ASN cc_start: 0.7589 (m-40) cc_final: 0.7279 (m-40) REVERT: B 100 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 119 ASN cc_start: 0.8274 (m-40) cc_final: 0.8066 (m110) REVERT: B 186 ASP cc_start: 0.7716 (m-30) cc_final: 0.7404 (m-30) REVERT: B 212 ASP cc_start: 0.7896 (t0) cc_final: 0.7580 (t0) REVERT: B 258 ASP cc_start: 0.7996 (t0) cc_final: 0.7438 (t0) REVERT: B 314 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7931 (ptm160) REVERT: B 315 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7813 (p) REVERT: R 17 PHE cc_start: 0.8524 (t80) cc_final: 0.8217 (t80) outliers start: 42 outliers final: 15 residues processed: 242 average time/residue: 1.1137 time to fit residues: 286.9562 Evaluate side-chains 241 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 235 THR Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 92 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 126 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 155 ASN B 176 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8545 Z= 0.195 Angle : 0.534 7.422 11572 Z= 0.282 Chirality : 0.040 0.188 1307 Planarity : 0.004 0.036 1450 Dihedral : 4.323 34.849 1211 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 3.86 % Allowed : 23.62 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.26), residues: 1038 helix: 2.69 (0.23), residues: 439 sheet: 0.01 (0.36), residues: 217 loop : -0.88 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.019 0.002 PHE R 82 TYR 0.011 0.001 TYR N 96 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7143 (mtm-85) REVERT: A 236 ASP cc_start: 0.8666 (t70) cc_final: 0.8368 (t0) REVERT: B 46 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7236 (mtp-110) REVERT: B 100 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 176 GLN cc_start: 0.8554 (mt0) cc_final: 0.8349 (mt0) REVERT: B 186 ASP cc_start: 0.7589 (m-30) cc_final: 0.7298 (m-30) REVERT: B 212 ASP cc_start: 0.7821 (t0) cc_final: 0.7621 (t0) REVERT: B 258 ASP cc_start: 0.7961 (t0) cc_final: 0.7303 (t0) REVERT: B 283 ARG cc_start: 0.8393 (tpt-90) cc_final: 0.8123 (tpt90) REVERT: B 314 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7863 (ptm160) REVERT: R 17 PHE cc_start: 0.8592 (t80) cc_final: 0.8217 (t80) outliers start: 35 outliers final: 16 residues processed: 236 average time/residue: 1.2032 time to fit residues: 302.9814 Evaluate side-chains 240 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 88 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8545 Z= 0.239 Angle : 0.550 7.708 11572 Z= 0.288 Chirality : 0.041 0.182 1307 Planarity : 0.004 0.038 1450 Dihedral : 4.339 34.814 1211 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 3.53 % Allowed : 24.50 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.26), residues: 1038 helix: 2.64 (0.23), residues: 441 sheet: 0.11 (0.36), residues: 203 loop : -0.90 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.002 PHE A 87 TYR 0.013 0.001 TYR N 96 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: A 134 ASN cc_start: 0.7471 (t0) cc_final: 0.7185 (m-40) REVERT: B 46 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7240 (mtp-110) REVERT: B 101 MET cc_start: 0.8419 (mtm) cc_final: 0.8163 (mtt) REVERT: B 186 ASP cc_start: 0.7685 (m-30) cc_final: 0.7314 (m-30) REVERT: B 212 ASP cc_start: 0.7842 (t0) cc_final: 0.7609 (t0) REVERT: B 258 ASP cc_start: 0.7972 (t0) cc_final: 0.7290 (t0) REVERT: B 283 ARG cc_start: 0.8436 (tpt-90) cc_final: 0.8157 (tpt90) REVERT: B 314 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7899 (ptm160) REVERT: R 17 PHE cc_start: 0.8652 (t80) cc_final: 0.8154 (t80) REVERT: R 99 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8440 (tp) outliers start: 32 outliers final: 13 residues processed: 244 average time/residue: 1.1463 time to fit residues: 297.4916 Evaluate side-chains 236 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 126 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 88 ASN B 119 ASN B 155 ASN B 176 GLN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8545 Z= 0.288 Angle : 0.575 8.573 11572 Z= 0.302 Chirality : 0.042 0.191 1307 Planarity : 0.004 0.040 1450 Dihedral : 4.466 34.921 1211 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.42 % Allowed : 24.61 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.26), residues: 1038 helix: 2.60 (0.23), residues: 440 sheet: 0.09 (0.36), residues: 209 loop : -0.93 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.002 PHE R 82 TYR 0.015 0.001 TYR N 96 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 223 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7185 (mtm-85) REVERT: A 203 ILE cc_start: 0.8516 (mt) cc_final: 0.8256 (mp) REVERT: B 46 ARG cc_start: 0.7496 (mtt-85) cc_final: 0.7227 (mtp-110) REVERT: B 186 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: B 212 ASP cc_start: 0.7827 (t0) cc_final: 0.7578 (t0) REVERT: B 258 ASP cc_start: 0.7996 (t0) cc_final: 0.7301 (t0) REVERT: B 283 ARG cc_start: 0.8429 (tpt-90) cc_final: 0.8208 (tpt90) REVERT: B 314 ARG cc_start: 0.8166 (ptm160) cc_final: 0.7872 (ptm160) REVERT: R 17 PHE cc_start: 0.8686 (t80) cc_final: 0.8206 (t80) REVERT: R 58 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8011 (tp) outliers start: 40 outliers final: 16 residues processed: 241 average time/residue: 1.1836 time to fit residues: 303.1613 Evaluate side-chains 236 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 chunk 82 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN B 119 ASN B 155 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8545 Z= 0.207 Angle : 0.555 8.177 11572 Z= 0.290 Chirality : 0.041 0.186 1307 Planarity : 0.004 0.037 1450 Dihedral : 4.345 34.954 1211 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 3.97 % Allowed : 25.06 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.26), residues: 1038 helix: 2.67 (0.23), residues: 439 sheet: -0.01 (0.35), residues: 217 loop : -0.97 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.023 0.002 PHE R 82 TYR 0.011 0.001 TYR N 96 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7164 (mtm-85) REVERT: A 203 ILE cc_start: 0.8460 (mt) cc_final: 0.8198 (mp) REVERT: B 100 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 119 ASN cc_start: 0.7918 (m-40) cc_final: 0.7713 (m110) REVERT: B 137 ARG cc_start: 0.7572 (mmt-90) cc_final: 0.7229 (tpt170) REVERT: B 186 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: B 212 ASP cc_start: 0.7823 (t0) cc_final: 0.7550 (t0) REVERT: B 237 ASN cc_start: 0.8456 (t0) cc_final: 0.8129 (t160) REVERT: B 239 ASN cc_start: 0.8212 (m110) cc_final: 0.7823 (m110) REVERT: B 258 ASP cc_start: 0.7955 (t0) cc_final: 0.7221 (t0) REVERT: B 283 ARG cc_start: 0.8427 (tpt-90) cc_final: 0.8222 (tpt90) REVERT: B 314 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7809 (ptm160) REVERT: C 37 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (mp) REVERT: R 17 PHE cc_start: 0.8447 (t80) cc_final: 0.8235 (t80) REVERT: R 58 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7975 (tp) outliers start: 36 outliers final: 16 residues processed: 241 average time/residue: 1.1445 time to fit residues: 293.4917 Evaluate side-chains 241 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 134 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 176 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8545 Z= 0.267 Angle : 0.596 8.162 11572 Z= 0.311 Chirality : 0.043 0.185 1307 Planarity : 0.004 0.039 1450 Dihedral : 4.467 34.844 1211 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 3.75 % Allowed : 26.05 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.26), residues: 1038 helix: 2.61 (0.23), residues: 439 sheet: 0.06 (0.36), residues: 203 loop : -0.98 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.024 0.002 PHE R 82 TYR 0.014 0.001 TYR N 96 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 220 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7189 (mtm-85) REVERT: A 188 ARG cc_start: 0.7548 (pmm-80) cc_final: 0.7307 (mpp80) REVERT: A 203 ILE cc_start: 0.8504 (mt) cc_final: 0.8245 (mp) REVERT: A 236 ASP cc_start: 0.8638 (t70) cc_final: 0.8254 (t0) REVERT: B 186 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: B 212 ASP cc_start: 0.7801 (t0) cc_final: 0.7541 (t0) REVERT: B 258 ASP cc_start: 0.7971 (t0) cc_final: 0.7140 (t0) REVERT: B 283 ARG cc_start: 0.8411 (tpt-90) cc_final: 0.8165 (tpt90) REVERT: C 37 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8182 (mp) REVERT: R 17 PHE cc_start: 0.8526 (t80) cc_final: 0.8290 (t80) REVERT: R 58 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8068 (tp) outliers start: 34 outliers final: 17 residues processed: 235 average time/residue: 1.1353 time to fit residues: 283.9612 Evaluate side-chains 235 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 9 optimal weight: 0.0170 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 88 ASN B 119 ASN B 155 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8545 Z= 0.238 Angle : 0.591 7.648 11572 Z= 0.309 Chirality : 0.042 0.182 1307 Planarity : 0.004 0.038 1450 Dihedral : 4.432 34.772 1211 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 3.42 % Allowed : 26.60 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.26), residues: 1038 helix: 2.64 (0.23), residues: 437 sheet: 0.06 (0.36), residues: 203 loop : -1.02 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.027 0.002 PHE B 278 TYR 0.013 0.001 TYR N 96 ARG 0.010 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 230 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: A 134 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6940 (m110) REVERT: A 203 ILE cc_start: 0.8485 (mt) cc_final: 0.8226 (mp) REVERT: A 211 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7247 (mtm-85) REVERT: A 213 TYR cc_start: 0.8420 (m-80) cc_final: 0.8088 (m-80) REVERT: A 236 ASP cc_start: 0.8684 (t70) cc_final: 0.8360 (t0) REVERT: B 72 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 119 ASN cc_start: 0.7941 (m-40) cc_final: 0.7709 (m110) REVERT: B 186 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: B 212 ASP cc_start: 0.7810 (t0) cc_final: 0.7555 (t0) REVERT: B 237 ASN cc_start: 0.8488 (t0) cc_final: 0.8160 (t160) REVERT: B 239 ASN cc_start: 0.8245 (m110) cc_final: 0.7859 (m110) REVERT: B 258 ASP cc_start: 0.7965 (t0) cc_final: 0.7234 (t0) REVERT: B 278 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8134 (m-10) REVERT: B 283 ARG cc_start: 0.8358 (tpt-90) cc_final: 0.8133 (tpt90) REVERT: B 314 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7873 (ptm160) REVERT: B 340 ASN cc_start: 0.7745 (t0) cc_final: 0.7462 (t0) REVERT: R 58 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8065 (tp) outliers start: 31 outliers final: 19 residues processed: 243 average time/residue: 1.1581 time to fit residues: 301.4648 Evaluate side-chains 253 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 88 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8545 Z= 0.256 Angle : 0.610 7.661 11572 Z= 0.318 Chirality : 0.043 0.182 1307 Planarity : 0.004 0.042 1450 Dihedral : 4.483 34.852 1211 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 3.20 % Allowed : 27.26 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.26), residues: 1038 helix: 2.58 (0.23), residues: 439 sheet: 0.02 (0.36), residues: 203 loop : -1.05 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.037 0.002 PHE R 17 TYR 0.014 0.001 TYR N 96 ARG 0.009 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 227 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8328 (p0) cc_final: 0.8127 (p0) REVERT: A 120 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7213 (mtm-85) REVERT: A 203 ILE cc_start: 0.8491 (mt) cc_final: 0.8236 (mp) REVERT: A 211 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7225 (mtm-85) REVERT: A 236 ASP cc_start: 0.8667 (t70) cc_final: 0.8338 (t0) REVERT: B 72 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 186 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: B 212 ASP cc_start: 0.7839 (t0) cc_final: 0.7542 (t0) REVERT: B 258 ASP cc_start: 0.7962 (t0) cc_final: 0.7270 (t0) REVERT: B 283 ARG cc_start: 0.8370 (tpt-90) cc_final: 0.8129 (tpt90) REVERT: B 314 ARG cc_start: 0.8166 (ptm160) cc_final: 0.7857 (ptm160) REVERT: B 340 ASN cc_start: 0.7764 (t0) cc_final: 0.7479 (t0) REVERT: R 58 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8047 (tp) outliers start: 29 outliers final: 19 residues processed: 238 average time/residue: 1.1546 time to fit residues: 291.9270 Evaluate side-chains 249 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 226 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 119 ASN B 155 ASN B 237 ASN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8545 Z= 0.213 Angle : 0.602 7.700 11572 Z= 0.314 Chirality : 0.043 0.197 1307 Planarity : 0.004 0.040 1450 Dihedral : 4.438 34.895 1211 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 2.76 % Allowed : 28.15 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.26), residues: 1038 helix: 2.66 (0.23), residues: 439 sheet: 0.06 (0.36), residues: 203 loop : -1.06 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.035 0.002 PHE R 17 TYR 0.013 0.001 TYR B 124 ARG 0.009 0.001 ARG A 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.8334 (p0) cc_final: 0.8130 (p0) REVERT: A 120 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7195 (mtm-85) REVERT: A 203 ILE cc_start: 0.8460 (mt) cc_final: 0.8190 (mp) REVERT: A 211 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7236 (mtm-85) REVERT: A 213 TYR cc_start: 0.8387 (m-80) cc_final: 0.8003 (m-80) REVERT: A 236 ASP cc_start: 0.8661 (t70) cc_final: 0.8345 (t0) REVERT: B 72 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 119 ASN cc_start: 0.7877 (m-40) cc_final: 0.7624 (m110) REVERT: B 186 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: B 212 ASP cc_start: 0.7827 (t0) cc_final: 0.7571 (t0) REVERT: B 237 ASN cc_start: 0.8426 (t0) cc_final: 0.8120 (t160) REVERT: B 239 ASN cc_start: 0.8206 (m110) cc_final: 0.7785 (m110) REVERT: B 258 ASP cc_start: 0.7913 (t0) cc_final: 0.7111 (t0) REVERT: B 283 ARG cc_start: 0.8302 (tpt-90) cc_final: 0.7991 (tpt90) REVERT: B 314 ARG cc_start: 0.8082 (ptm160) cc_final: 0.7798 (ptm160) REVERT: B 340 ASN cc_start: 0.7753 (t0) cc_final: 0.7485 (t0) REVERT: R 58 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8018 (tp) REVERT: R 205 MET cc_start: 0.8250 (ttp) cc_final: 0.8037 (ttm) REVERT: R 235 THR cc_start: 0.8492 (t) cc_final: 0.8266 (t) outliers start: 25 outliers final: 18 residues processed: 241 average time/residue: 1.0955 time to fit residues: 281.3408 Evaluate side-chains 248 residues out of total 906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 175 PHE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 192 THR Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 75 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120039 restraints weight = 11947.028| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.05 r_work: 0.3404 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8545 Z= 0.258 Angle : 0.618 7.795 11572 Z= 0.322 Chirality : 0.043 0.195 1307 Planarity : 0.004 0.040 1450 Dihedral : 4.542 34.792 1211 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.85 % Favored : 95.95 % Rotamer: Outliers : 2.76 % Allowed : 28.70 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.26), residues: 1038 helix: 2.61 (0.23), residues: 439 sheet: -0.01 (0.36), residues: 203 loop : -1.05 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 99 HIS 0.003 0.001 HIS A 212 PHE 0.041 0.002 PHE B 278 TYR 0.022 0.002 TYR N 61 ARG 0.010 0.001 ARG A 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4579.14 seconds wall clock time: 80 minutes 6.99 seconds (4806.99 seconds total)