Starting phenix.real_space_refine on Mon Apr 8 16:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/04_2024/8u8f_42023_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/04_2024/8u8f_42023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/04_2024/8u8f_42023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/04_2024/8u8f_42023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/04_2024/8u8f_42023_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8f_42023/04_2024/8u8f_42023_trim_updated.pdb" } resolution = 3.49 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= -0.003 sd= 0.065 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: 5 Type Number sf(0) Gaussians S 49 5.16 5 C 4433 2.51 5 N 1209 2.21 5 O 1275 1.98 5 H 6925 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13891 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3800 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5094 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4094 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 1 Chain: "R" Number of atoms: 32 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 16 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 1, 16 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" CA APLM R 401 " occ=0.68 ... (30 atoms not shown) pdb=" CF BPLM R 401 " occ=0.32 Time building chain proxies: 6.74, per 1000 atoms: 0.49 Number of scatterers: 13891 At special positions: 0 Unit cell: (78.26, 100.62, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 O 1275 8.00 N 1209 7.00 C 4433 6.00 H 6925 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 177 " - pdb=" SG CYS R 184 " distance=2.04 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: 12.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 8 sheets defined 40.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.552A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.999A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.330A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 45 through 67 removed outlier: 3.529A pdb=" N LEU R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 100 Processing helix chain 'R' and resid 106 through 139 removed outlier: 4.042A pdb=" N LEU R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 168 Processing helix chain 'R' and resid 192 through 230 removed outlier: 3.549A pdb=" N LEU R 229 " --> pdb=" O GLN R 225 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 252 removed outlier: 3.655A pdb=" N VAL R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 269 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 276 through 297 removed outlier: 3.709A pdb=" N THR R 282 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU R 284 " --> pdb=" O LEU R 281 " (cutoff:3.500A) Proline residue: R 285 - end of helix removed outlier: 3.524A pdb=" N ILE R 292 " --> pdb=" O ASN R 289 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN R 293 " --> pdb=" O SER R 290 " (cutoff:3.500A) Proline residue: R 294 - end of helix removed outlier: 3.767A pdb=" N TYR R 297 " --> pdb=" O PRO R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 312 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 291 removed outlier: 9.805A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 83 Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.682A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.150A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.661A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.837A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.537A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.790A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 903 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: 4.91 Time building geometry restraints manager: 12.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6897 1.04 - 1.23: 246 1.23 - 1.43: 2748 1.43 - 1.63: 4065 1.63 - 1.83: 68 Bond restraints: 14024 Sorted by residual: bond pdb=" N VAL R 132 " pdb=" CA VAL R 132 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.90e+00 bond pdb=" N LEU R 136 " pdb=" H LEU R 136 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" N ALA R 129 " pdb=" H ALA R 129 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" N VAL R 155 " pdb=" H VAL R 155 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" N LEU R 78 " pdb=" H LEU R 78 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 14019 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.69: 3 85.69 - 97.84: 0 97.84 - 109.98: 11947 109.98 - 122.12: 11001 122.12 - 134.26: 2293 Bond angle restraints: 25244 Sorted by residual: angle pdb=" C ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 109.00 73.55 35.45 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 110.00 74.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 109.00 79.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" CD PRO G 49 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" N ASN B 313 " pdb=" CA ASN B 313 " pdb=" CB ASN B 313 " ideal model delta sigma weight residual 114.17 109.59 4.58 1.14e+00 7.69e-01 1.62e+01 ... (remaining 25239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5908 17.91 - 35.83: 502 35.83 - 53.74: 143 53.74 - 71.66: 36 71.66 - 89.57: 14 Dihedral angle restraints: 6603 sinusoidal: 3564 harmonic: 3039 Sorted by residual: dihedral pdb=" CB CYS R 177 " pdb=" SG CYS R 177 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual -86.00 -26.65 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CA ASN R 176 " pdb=" C ASN R 176 " pdb=" N CYS R 177 " pdb=" CA CYS R 177 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA VAL R 187 " pdb=" C VAL R 187 " pdb=" N TYR R 188 " pdb=" CA TYR R 188 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1050 0.091 - 0.182: 53 0.182 - 0.273: 0 0.273 - 0.364: 0 0.364 - 0.455: 1 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA ASN B 340 " pdb=" N ASN B 340 " pdb=" C ASN B 340 " pdb=" CB ASN B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL R 155 " pdb=" N VAL R 155 " pdb=" C VAL R 155 " pdb=" CB VAL R 155 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA LEU R 159 " pdb=" N LEU R 159 " pdb=" C LEU R 159 " pdb=" CB LEU R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1101 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 152 " 0.447 9.50e-02 1.11e+02 1.51e-01 3.60e+01 pdb=" NE ARG R 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG R 152 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 152 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 152 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG R 152 " -0.048 2.00e-02 2.50e+03 pdb="HH12 ARG R 152 " 0.051 2.00e-02 2.50e+03 pdb="HH21 ARG R 152 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG R 152 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO G 49 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 136 " 0.013 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" N SER R 137 " -0.042 2.00e-02 2.50e+03 pdb=" CA SER R 137 " 0.011 2.00e-02 2.50e+03 pdb=" H SER R 137 " 0.018 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 729 2.18 - 2.79: 27808 2.79 - 3.39: 39234 3.39 - 4.00: 49387 4.00 - 4.60: 77382 Nonbonded interactions: 194540 Sorted by model distance: nonbonded pdb=" O TYR R 266 " pdb=" H GLY R 270 " model vdw 1.579 1.850 nonbonded pdb=" OD1 ASN R 176 " pdb=" H SER R 191 " model vdw 1.600 1.850 nonbonded pdb=" O ASN R 140 " pdb=" H TYR R 144 " model vdw 1.634 1.850 nonbonded pdb=" OD1 ASP R 179 " pdb=" H LEU R 181 " model vdw 1.662 1.850 nonbonded pdb="HH21 ARG A 38 " pdb=" OE2 GLU R 147 " model vdw 1.666 1.850 ... (remaining 194535 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: 0.010 Normalize map: mean=0, sd=1: 0.810 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: 0.190 Extract box with map and model: 4.360 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 49.690 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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 0.109 7099 Z= 0.217 Angle : 0.544 10.634 9616 Z= 0.326 Chirality : 0.042 0.455 1104 Planarity : 0.007 0.182 1219 Dihedral : 15.464 89.571 2563 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 19.46 % Favored : 80.40 % 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: 1.41 (0.30), residues: 875 helix: 2.63 (0.28), residues: 358 sheet: 0.14 (0.42), residues: 156 loop : -0.42 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.000 HIS R 223 PHE 0.013 0.001 PHE R 299 TYR 0.024 0.001 TYR R 139 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.4726 time to fit residues: 85.2267 Evaluate side-chains 132 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7099 Z= 0.175 Angle : 0.490 10.235 9616 Z= 0.260 Chirality : 0.040 0.445 1104 Planarity : 0.004 0.074 1219 Dihedral : 4.329 50.629 992 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 1.61 % Allowed : 18.52 % Favored : 79.87 % 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: 1.32 (0.30), residues: 875 helix: 2.81 (0.27), residues: 359 sheet: -0.63 (0.41), residues: 163 loop : -0.39 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.004 0.001 HIS R 223 PHE 0.019 0.001 PHE A 246 TYR 0.008 0.001 TYR B 124 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7021 (m-10) cc_final: 0.6721 (m-10) REVERT: R 56 CYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6985 (m) outliers start: 12 outliers final: 7 residues processed: 145 average time/residue: 0.4138 time to fit residues: 78.2960 Evaluate side-chains 142 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7099 Z= 0.178 Angle : 0.487 10.431 9616 Z= 0.258 Chirality : 0.040 0.446 1104 Planarity : 0.004 0.066 1219 Dihedral : 4.375 47.131 992 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 2.82 % Allowed : 17.72 % Favored : 79.46 % 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: 1.22 (0.30), residues: 875 helix: 2.81 (0.27), residues: 357 sheet: -0.78 (0.41), residues: 169 loop : -0.46 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.014 0.001 PHE B 241 TYR 0.014 0.001 TYR A 311 ARG 0.011 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7119 (m-10) cc_final: 0.6697 (m-10) REVERT: R 56 CYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7004 (m) outliers start: 21 outliers final: 12 residues processed: 150 average time/residue: 0.4919 time to fit residues: 94.5604 Evaluate side-chains 146 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7099 Z= 0.147 Angle : 0.463 10.226 9616 Z= 0.245 Chirality : 0.040 0.445 1104 Planarity : 0.004 0.060 1219 Dihedral : 4.285 46.328 992 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.42 % Allowed : 18.39 % Favored : 79.19 % 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: 1.23 (0.30), residues: 875 helix: 2.91 (0.27), residues: 358 sheet: -0.97 (0.40), residues: 177 loop : -0.44 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR A 311 ARG 0.005 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7102 (m-10) cc_final: 0.6663 (m-10) REVERT: R 56 CYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7065 (m) outliers start: 18 outliers final: 14 residues processed: 149 average time/residue: 0.5011 time to fit residues: 96.2328 Evaluate side-chains 150 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 191 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.6989 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7099 Z= 0.280 Angle : 0.554 10.440 9616 Z= 0.299 Chirality : 0.042 0.441 1104 Planarity : 0.004 0.060 1219 Dihedral : 5.029 45.687 992 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 2.82 % Allowed : 19.60 % Favored : 77.58 % 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: 0.67 (0.30), residues: 875 helix: 2.42 (0.28), residues: 360 sheet: -1.42 (0.40), residues: 169 loop : -0.67 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.004 0.001 HIS R 223 PHE 0.026 0.002 PHE B 241 TYR 0.013 0.001 TYR B 264 ARG 0.011 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6680 (t70) cc_final: 0.6398 (t0) REVERT: B 44 GLN cc_start: 0.7473 (mt0) cc_final: 0.7189 (mt0) REVERT: B 63 TRP cc_start: 0.7183 (m-10) cc_final: 0.6620 (m-10) REVERT: R 56 CYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7082 (m) REVERT: R 146 SER cc_start: 0.8715 (t) cc_final: 0.8468 (p) outliers start: 21 outliers final: 19 residues processed: 144 average time/residue: 0.5042 time to fit residues: 92.5453 Evaluate side-chains 151 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.6936 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7099 Z= 0.167 Angle : 0.488 10.173 9616 Z= 0.261 Chirality : 0.040 0.443 1104 Planarity : 0.004 0.064 1219 Dihedral : 4.646 44.798 992 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 2.95 % Allowed : 20.13 % Favored : 76.91 % 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: 0.78 (0.30), residues: 875 helix: 2.59 (0.27), residues: 360 sheet: -1.44 (0.39), residues: 175 loop : -0.64 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.015 0.002 PHE A 290 TYR 0.012 0.001 TYR A 311 ARG 0.009 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6568 (t70) cc_final: 0.6315 (t0) REVERT: B 63 TRP cc_start: 0.7119 (m-10) cc_final: 0.6591 (m-10) REVERT: R 56 CYS cc_start: 0.7301 (OUTLIER) cc_final: 0.7068 (m) outliers start: 22 outliers final: 19 residues processed: 143 average time/residue: 0.5176 time to fit residues: 94.9489 Evaluate side-chains 147 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7099 Z= 0.149 Angle : 0.470 10.167 9616 Z= 0.249 Chirality : 0.040 0.444 1104 Planarity : 0.004 0.075 1219 Dihedral : 4.390 44.649 992 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 20.81 % Favored : 76.64 % 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 (0.30), residues: 875 helix: 2.82 (0.27), residues: 360 sheet: -1.39 (0.39), residues: 175 loop : -0.57 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.014 0.001 PHE A 290 TYR 0.011 0.001 TYR A 311 ARG 0.011 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLN cc_start: 0.7492 (mt0) cc_final: 0.7144 (mt0) REVERT: B 63 TRP cc_start: 0.7108 (m-10) cc_final: 0.6543 (m-10) REVERT: R 56 CYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7073 (m) outliers start: 19 outliers final: 15 residues processed: 146 average time/residue: 0.5260 time to fit residues: 99.6259 Evaluate side-chains 141 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.6951 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7099 Z= 0.200 Angle : 0.504 10.228 9616 Z= 0.268 Chirality : 0.041 0.442 1104 Planarity : 0.004 0.072 1219 Dihedral : 4.637 44.296 992 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.57 % Favored : 95.31 % Rotamer: Outliers : 2.55 % Allowed : 21.48 % Favored : 75.97 % 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: 0.77 (0.30), residues: 875 helix: 2.67 (0.28), residues: 360 sheet: -1.57 (0.38), residues: 177 loop : -0.67 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.017 0.002 PHE B 241 TYR 0.010 0.001 TYR A 311 ARG 0.011 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6678 (t70) cc_final: 0.6412 (t0) REVERT: B 44 GLN cc_start: 0.7503 (mt0) cc_final: 0.7192 (mt0) REVERT: B 63 TRP cc_start: 0.7127 (m-10) cc_final: 0.6559 (m-10) REVERT: R 56 CYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7067 (m) outliers start: 19 outliers final: 18 residues processed: 137 average time/residue: 0.5172 time to fit residues: 90.3579 Evaluate side-chains 143 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7099 Z= 0.151 Angle : 0.480 10.251 9616 Z= 0.254 Chirality : 0.040 0.446 1104 Planarity : 0.004 0.079 1219 Dihedral : 4.183 35.703 990 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.01 % Allowed : 22.01 % Favored : 75.97 % 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: 0.95 (0.30), residues: 875 helix: 2.81 (0.27), residues: 360 sheet: -1.38 (0.39), residues: 172 loop : -0.63 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS R 223 PHE 0.012 0.001 PHE A 290 TYR 0.010 0.001 TYR A 311 ARG 0.010 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6549 (t70) cc_final: 0.6288 (t0) REVERT: B 44 GLN cc_start: 0.7453 (mt0) cc_final: 0.7109 (mt0) REVERT: B 63 TRP cc_start: 0.7092 (m-10) cc_final: 0.6525 (m-10) REVERT: R 56 CYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7055 (m) outliers start: 15 outliers final: 14 residues processed: 134 average time/residue: 0.5384 time to fit residues: 91.5317 Evaluate side-chains 137 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7022 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7099 Z= 0.294 Angle : 0.575 10.262 9616 Z= 0.310 Chirality : 0.042 0.436 1104 Planarity : 0.005 0.072 1219 Dihedral : 4.994 42.152 990 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.26 % Rotamer: Outliers : 2.42 % Allowed : 21.74 % Favored : 75.84 % 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: 0.31 (0.30), residues: 875 helix: 2.30 (0.27), residues: 360 sheet: -1.89 (0.38), residues: 175 loop : -0.88 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.004 0.001 HIS R 223 PHE 0.025 0.002 PHE B 241 TYR 0.012 0.001 TYR B 264 ARG 0.011 0.001 ARG R 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.6767 (t70) cc_final: 0.6500 (t0) REVERT: B 63 TRP cc_start: 0.7175 (m-10) cc_final: 0.6640 (m-10) REVERT: B 75 GLN cc_start: 0.8108 (mt0) cc_final: 0.7787 (mt0) REVERT: B 171 ILE cc_start: 0.7134 (mm) cc_final: 0.6872 (mm) REVERT: R 56 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.7035 (m) outliers start: 18 outliers final: 16 residues processed: 133 average time/residue: 0.5409 time to fit residues: 91.1421 Evaluate side-chains 137 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.185719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150559 restraints weight = 24214.198| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.98 r_work: 0.3736 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7099 Z= 0.140 Angle : 0.481 10.195 9616 Z= 0.254 Chirality : 0.040 0.448 1104 Planarity : 0.004 0.081 1219 Dihedral : 4.261 34.327 990 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.28 % Allowed : 21.88 % Favored : 75.84 % 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: 0.79 (0.30), residues: 875 helix: 2.70 (0.27), residues: 360 sheet: -1.53 (0.39), residues: 171 loop : -0.71 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS B 311 PHE 0.013 0.001 PHE A 290 TYR 0.009 0.001 TYR A 311 ARG 0.010 0.001 ARG R 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.55 seconds wall clock time: 74 minutes 51.34 seconds (4491.34 seconds total)