Starting phenix.real_space_refine on Wed Mar 12 02:04:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chx_45604/03_2025/9chx_45604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chx_45604/03_2025/9chx_45604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chx_45604/03_2025/9chx_45604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chx_45604/03_2025/9chx_45604.map" model { file = "/net/cci-nas-00/data/ceres_data/9chx_45604/03_2025/9chx_45604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chx_45604/03_2025/9chx_45604.cif" } resolution = 3.5 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= 0.010 sd= 0.075 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 4644 2.51 5 N 1164 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7129 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3450 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 422} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2792 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 20, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'CAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.72 Number of scatterers: 7129 At special positions: 0 Unit cell: (68.85, 84.15, 155.55, 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 1273 8.00 N 1164 7.00 C 4644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.06 Conformation dependent library (CDL) restraints added in 977.0 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 32 through 60 removed outlier: 3.581A pdb=" N ILE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 97 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 103 through 137 removed outlier: 3.907A pdb=" N GLU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 146 through 171 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 226 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.801A pdb=" N ALA A 232 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.882A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.928A pdb=" N LYS A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.791A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 394 through 421 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 429 through 444 removed outlier: 4.127A pdb=" N ASN A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.520A pdb=" N ILE A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.800A pdb=" N ILE A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 4.028A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.577A pdb=" N THR B 156 " --> pdb=" O CYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.695A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.709A pdb=" N LEU B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.779A pdb=" N MET B 346 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 Processing helix chain 'B' and resid 353 through 369 removed outlier: 3.514A pdb=" N GLU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 removed outlier: 3.965A pdb=" N ALA C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.502A pdb=" N ILE B 80 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.984A pdb=" N VAL C 4 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR C 75 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N THR C 6 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS C 73 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 98 " --> pdb=" O MET C 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.237A pdb=" N HIS C 25 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU C 103 " --> pdb=" O HIS C 25 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 978 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: 1.84 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2232 1.34 - 1.46: 1723 1.46 - 1.58: 3277 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7305 Sorted by residual: bond pdb=" C13 CAU A 501 " pdb=" O14 CAU A 501 " ideal model delta sigma weight residual 1.342 1.399 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" N SER A 203 " pdb=" CA SER A 203 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.83e+00 bond pdb=" C3 CAU A 501 " pdb=" C4 CAU A 501 " ideal model delta sigma weight residual 1.412 1.372 0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C8 CAU A 501 " pdb=" C9 CAU A 501 " ideal model delta sigma weight residual 1.406 1.371 0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" CA SER A 203 " pdb=" CB SER A 203 " ideal model delta sigma weight residual 1.528 1.504 0.025 1.56e-02 4.11e+03 2.49e+00 ... (remaining 7300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 9777 2.30 - 4.59: 111 4.59 - 6.89: 19 6.89 - 9.19: 2 9.19 - 11.49: 3 Bond angle restraints: 9912 Sorted by residual: angle pdb=" C6 FK5 C 201 " pdb=" N7 FK5 C 201 " pdb=" C8 FK5 C 201 " ideal model delta sigma weight residual 109.47 120.96 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C2 FK5 C 201 " pdb=" N7 FK5 C 201 " pdb=" C6 FK5 C 201 " ideal model delta sigma weight residual 109.47 120.48 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N GLN B 193 " pdb=" CA GLN B 193 " pdb=" C GLN B 193 " ideal model delta sigma weight residual 114.56 110.40 4.16 1.27e+00 6.20e-01 1.07e+01 angle pdb=" C2 FK5 C 201 " pdb=" N7 FK5 C 201 " pdb=" C8 FK5 C 201 " ideal model delta sigma weight residual 109.47 118.55 -9.08 3.00e+00 1.11e-01 9.16e+00 angle pdb=" CA LEU B 364 " pdb=" CB LEU B 364 " pdb=" CG LEU B 364 " ideal model delta sigma weight residual 116.30 106.32 9.98 3.50e+00 8.16e-02 8.14e+00 ... (remaining 9907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.86: 4219 33.86 - 67.71: 92 67.71 - 101.57: 7 101.57 - 135.43: 0 135.43 - 169.28: 2 Dihedral angle restraints: 4320 sinusoidal: 1734 harmonic: 2586 Sorted by residual: dihedral pdb=" O14 CAU A 501 " pdb=" C15 CAU A 501 " pdb=" C16 CAU A 501 " pdb=" O17 CAU A 501 " ideal model delta sinusoidal sigma weight residual 54.74 -135.98 -169.28 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C18 CAU A 501 " pdb=" C15 CAU A 501 " pdb=" C16 CAU A 501 " pdb=" O14 CAU A 501 " ideal model delta sinusoidal sigma weight residual 179.20 16.56 162.64 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA GLU A 62 " pdb=" C GLU A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 719 0.038 - 0.075: 313 0.075 - 0.113: 68 0.113 - 0.151: 13 0.151 - 0.189: 2 Chirality restraints: 1115 Sorted by residual: chirality pdb=" C16 CAU A 501 " pdb=" C15 CAU A 501 " pdb=" C18 CAU A 501 " pdb=" O17 CAU A 501 " both_signs ideal model delta sigma weight residual False 2.31 2.49 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CB ILE A 426 " pdb=" CA ILE A 426 " pdb=" CG1 ILE A 426 " pdb=" CG2 ILE A 426 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA PHE A 223 " pdb=" N PHE A 223 " pdb=" C PHE A 223 " pdb=" CB PHE A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1112 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 77 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 78 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 78 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 78 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 193 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C PHE A 193 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE A 193 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 194 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 280 " 0.011 2.00e-02 2.50e+03 1.06e-02 1.67e+00 pdb=" CG HIS B 280 " -0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS B 280 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 280 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 280 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 280 " 0.003 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 145 2.70 - 3.25: 7080 3.25 - 3.80: 10807 3.80 - 4.35: 13634 4.35 - 4.90: 23055 Nonbonded interactions: 54721 Sorted by model distance: nonbonded pdb=" OG SER B 293 " pdb=" O PHE B 298 " model vdw 2.146 3.040 nonbonded pdb=" OG SER A 323 " pdb=" O THR B 13 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR C 6 " pdb=" OE1 GLN C 70 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP A 231 " pdb=" NZ LYS A 236 " model vdw 2.313 3.120 ... (remaining 54716 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 group one per residue 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: 2.280 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.004 0.057 7305 Z= 0.237 Angle : 0.664 11.487 9912 Z= 0.349 Chirality : 0.043 0.189 1115 Planarity : 0.003 0.046 1248 Dihedral : 14.884 169.282 2646 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.53 (0.29), residues: 879 helix: 0.33 (0.25), residues: 444 sheet: -0.36 (0.60), residues: 74 loop : -1.13 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 109 HIS 0.011 0.001 HIS B 280 PHE 0.019 0.002 PHE A 223 TYR 0.012 0.001 TYR B 259 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: C 100 ASP cc_start: 0.7046 (t70) cc_final: 0.6704 (t0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1575 time to fit residues: 23.9602 Evaluate side-chains 79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.0070 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 435 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN C 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.198386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157504 restraints weight = 8228.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160010 restraints weight = 7219.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.162100 restraints weight = 6171.465| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7305 Z= 0.271 Angle : 0.650 11.936 9912 Z= 0.331 Chirality : 0.044 0.136 1115 Planarity : 0.004 0.077 1248 Dihedral : 8.818 142.211 1005 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.57 % Allowed : 11.01 % Favored : 87.42 % 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: -0.46 (0.29), residues: 879 helix: 0.39 (0.25), residues: 449 sheet: -0.61 (0.61), residues: 64 loop : -1.04 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 109 HIS 0.007 0.001 HIS B 280 PHE 0.019 0.002 PHE A 242 TYR 0.027 0.002 TYR B 174 ARG 0.002 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: C 100 ASP cc_start: 0.7388 (t70) cc_final: 0.6929 (t0) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.1674 time to fit residues: 19.8417 Evaluate side-chains 84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 284 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 0.0010 chunk 50 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.200177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156965 restraints weight = 8243.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.159257 restraints weight = 6093.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.162318 restraints weight = 4891.086| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7305 Z= 0.178 Angle : 0.578 11.429 9912 Z= 0.292 Chirality : 0.041 0.134 1115 Planarity : 0.004 0.058 1248 Dihedral : 7.991 121.050 1005 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.97 % Allowed : 15.07 % Favored : 82.96 % 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: -0.28 (0.29), residues: 879 helix: 0.61 (0.26), residues: 448 sheet: -1.15 (0.58), residues: 70 loop : -0.90 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 109 HIS 0.004 0.001 HIS C 94 PHE 0.016 0.001 PHE A 242 TYR 0.018 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.918 Fit side-chains REVERT: A 179 GLN cc_start: 0.8817 (pm20) cc_final: 0.8601 (tp-100) REVERT: A 208 PHE cc_start: 0.7907 (t80) cc_final: 0.7699 (t80) REVERT: B 322 LYS cc_start: 0.7840 (mttm) cc_final: 0.7546 (mttm) REVERT: C 100 ASP cc_start: 0.7357 (t70) cc_final: 0.6824 (t0) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.1547 time to fit residues: 20.0395 Evaluate side-chains 89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.198100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156599 restraints weight = 8379.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.158685 restraints weight = 6474.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.160958 restraints weight = 5703.371| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7305 Z= 0.211 Angle : 0.628 13.721 9912 Z= 0.315 Chirality : 0.042 0.215 1115 Planarity : 0.004 0.051 1248 Dihedral : 7.451 94.093 1005 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.23 % Allowed : 17.56 % Favored : 80.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 879 helix: 0.61 (0.25), residues: 448 sheet: -1.24 (0.58), residues: 70 loop : -0.91 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 109 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.001 PHE A 242 TYR 0.015 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.781 Fit side-chains REVERT: B 73 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: B 322 LYS cc_start: 0.7849 (mttm) cc_final: 0.7557 (mttm) REVERT: C 100 ASP cc_start: 0.7311 (t70) cc_final: 0.6724 (t0) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.1614 time to fit residues: 21.3353 Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** 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 = 0.4459 r_free = 0.4459 target = 0.200469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.159507 restraints weight = 8290.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.162339 restraints weight = 6504.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.164553 restraints weight = 5456.462| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7305 Z= 0.168 Angle : 0.589 11.341 9912 Z= 0.296 Chirality : 0.041 0.165 1115 Planarity : 0.004 0.047 1248 Dihedral : 6.911 74.175 1005 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.10 % Allowed : 18.48 % Favored : 79.42 % 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: -0.14 (0.29), residues: 879 helix: 0.76 (0.26), residues: 450 sheet: -1.22 (0.58), residues: 70 loop : -0.87 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 109 HIS 0.003 0.001 HIS B 280 PHE 0.014 0.001 PHE A 242 TYR 0.015 0.001 TYR B 139 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.4111 (OUTLIER) cc_final: 0.3902 (tt) REVERT: B 322 LYS cc_start: 0.7858 (mttm) cc_final: 0.7550 (mttm) REVERT: C 100 ASP cc_start: 0.7276 (t70) cc_final: 0.6725 (t0) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 0.1527 time to fit residues: 21.2951 Evaluate side-chains 88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.200406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.158842 restraints weight = 8241.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.160035 restraints weight = 6682.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162970 restraints weight = 5615.343| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7305 Z= 0.216 Angle : 0.617 11.649 9912 Z= 0.306 Chirality : 0.042 0.150 1115 Planarity : 0.004 0.068 1248 Dihedral : 6.813 59.279 1005 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.41 % Allowed : 18.61 % Favored : 77.98 % 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: -0.22 (0.29), residues: 879 helix: 0.64 (0.25), residues: 450 sheet: -0.92 (0.56), residues: 80 loop : -0.91 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 99 HIS 0.004 0.001 HIS B 280 PHE 0.013 0.001 PHE A 290 TYR 0.018 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.690 Fit side-chains REVERT: A 145 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3863 (tt) REVERT: B 73 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: B 174 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.7006 (t80) REVERT: B 281 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7446 (mm-30) REVERT: C 100 ASP cc_start: 0.7340 (t70) cc_final: 0.6759 (t0) outliers start: 26 outliers final: 14 residues processed: 94 average time/residue: 0.1607 time to fit residues: 21.9744 Evaluate side-chains 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 0.0010 chunk 44 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.203147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.164857 restraints weight = 8675.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.165165 restraints weight = 10306.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167513 restraints weight = 8482.990| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7305 Z= 0.161 Angle : 0.585 11.336 9912 Z= 0.291 Chirality : 0.041 0.135 1115 Planarity : 0.004 0.056 1248 Dihedral : 6.564 62.807 1005 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.28 % Allowed : 18.87 % Favored : 77.85 % 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: -0.12 (0.30), residues: 879 helix: 0.72 (0.25), residues: 452 sheet: -0.93 (0.56), residues: 80 loop : -0.85 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 99 HIS 0.004 0.001 HIS C 94 PHE 0.013 0.001 PHE A 242 TYR 0.019 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.786 Fit side-chains REVERT: A 145 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4331 (tt) REVERT: A 362 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6642 (mtp85) REVERT: B 73 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: B 174 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.7010 (t80) REVERT: B 322 LYS cc_start: 0.8026 (mttm) cc_final: 0.7742 (mttm) REVERT: C 100 ASP cc_start: 0.7292 (t70) cc_final: 0.6813 (t0) outliers start: 25 outliers final: 15 residues processed: 101 average time/residue: 0.1601 time to fit residues: 23.0735 Evaluate side-chains 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 280 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 0.0040 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.204923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.168284 restraints weight = 8664.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.168423 restraints weight = 10025.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.170737 restraints weight = 8597.887| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7305 Z= 0.153 Angle : 0.591 11.256 9912 Z= 0.293 Chirality : 0.041 0.212 1115 Planarity : 0.004 0.048 1248 Dihedral : 6.507 66.871 1005 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.28 % Allowed : 19.79 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.06 (0.30), residues: 879 helix: 0.80 (0.26), residues: 449 sheet: -0.93 (0.56), residues: 80 loop : -0.83 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 99 HIS 0.004 0.001 HIS B 280 PHE 0.012 0.001 PHE A 242 TYR 0.018 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.761 Fit side-chains REVERT: B 73 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: B 174 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6950 (t80) REVERT: B 276 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 322 LYS cc_start: 0.8010 (mttm) cc_final: 0.7725 (mttm) REVERT: C 100 ASP cc_start: 0.7314 (t70) cc_final: 0.6834 (t0) outliers start: 25 outliers final: 16 residues processed: 98 average time/residue: 0.1592 time to fit residues: 22.3994 Evaluate side-chains 99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.198895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.161495 restraints weight = 8758.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163695 restraints weight = 9760.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.165487 restraints weight = 7696.386| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7305 Z= 0.262 Angle : 0.681 11.939 9912 Z= 0.337 Chirality : 0.044 0.182 1115 Planarity : 0.004 0.048 1248 Dihedral : 6.816 70.147 1005 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.75 % Allowed : 20.97 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.33 (0.29), residues: 879 helix: 0.54 (0.25), residues: 448 sheet: -1.06 (0.56), residues: 80 loop : -0.91 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 99 HIS 0.005 0.001 HIS B 280 PHE 0.016 0.002 PHE A 290 TYR 0.018 0.002 TYR B 174 ARG 0.002 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.783 Fit side-chains REVERT: A 145 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4402 (tt) REVERT: A 362 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6631 (mtp85) REVERT: B 73 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: B 276 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 322 LYS cc_start: 0.8058 (mttm) cc_final: 0.7762 (mttm) REVERT: C 100 ASP cc_start: 0.7404 (t70) cc_final: 0.6891 (t0) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.1625 time to fit residues: 21.9817 Evaluate side-chains 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 183 ASN B 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.201968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.163160 restraints weight = 8824.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.163886 restraints weight = 10054.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166184 restraints weight = 8124.691| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7305 Z= 0.185 Angle : 0.623 11.522 9912 Z= 0.306 Chirality : 0.042 0.169 1115 Planarity : 0.004 0.047 1248 Dihedral : 6.596 71.156 1005 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.15 % Allowed : 20.58 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.22 (0.29), residues: 879 helix: 0.64 (0.25), residues: 448 sheet: -1.02 (0.56), residues: 80 loop : -0.86 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 99 HIS 0.004 0.001 HIS B 280 PHE 0.013 0.001 PHE A 290 TYR 0.020 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.837 Fit side-chains REVERT: A 145 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.4356 (tt) REVERT: A 208 PHE cc_start: 0.7692 (t80) cc_final: 0.7451 (t80) REVERT: A 362 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6653 (mtp85) REVERT: B 73 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: B 174 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.7063 (t80) REVERT: B 276 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 322 LYS cc_start: 0.8109 (mttm) cc_final: 0.7858 (mttm) REVERT: C 100 ASP cc_start: 0.7362 (t70) cc_final: 0.6869 (t0) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.1655 time to fit residues: 21.8204 Evaluate side-chains 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 99 TRP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 22 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.203952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.165750 restraints weight = 8660.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.165860 restraints weight = 10153.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.169078 restraints weight = 8474.055| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7305 Z= 0.176 Angle : 0.623 12.613 9912 Z= 0.305 Chirality : 0.042 0.160 1115 Planarity : 0.004 0.047 1248 Dihedral : 6.498 73.432 1005 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.75 % Allowed : 20.97 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 879 helix: 0.70 (0.26), residues: 448 sheet: -1.00 (0.56), residues: 80 loop : -0.84 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 99 HIS 0.004 0.001 HIS B 280 PHE 0.022 0.001 PHE A 297 TYR 0.018 0.001 TYR B 174 ARG 0.002 0.000 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.90 seconds wall clock time: 39 minutes 8.70 seconds (2348.70 seconds total)