Starting phenix.real_space_refine on Wed Jun 4 15:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jdr_61397/06_2025/9jdr_61397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jdr_61397/06_2025/9jdr_61397.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/9jdr_61397/06_2025/9jdr_61397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jdr_61397/06_2025/9jdr_61397.map" model { file = "/net/cci-nas-00/data/ceres_data/9jdr_61397/06_2025/9jdr_61397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jdr_61397/06_2025/9jdr_61397.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= 0.001 sd= 0.042 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 20 5.16 5 C 2264 2.51 5 N 532 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3371 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3371 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.68, per 1000 atoms: 0.80 Number of scatterers: 3371 At special positions: 0 Unit cell: (75.9, 64.9, 83.6, 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 20 16.00 O 555 8.00 N 532 7.00 C 2264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.77 Conformation dependent library (CDL) restraints added in 411.7 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 70.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.638A pdb=" N ASN A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 removed outlier: 3.937A pdb=" N THR A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix removed outlier: 3.850A pdb=" N GLN A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.598A pdb=" N TYR A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 87 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 removed outlier: 3.623A pdb=" N LEU A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.741A pdb=" N VAL A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.649A pdb=" N GLY A 138 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.653A pdb=" N PHE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.668A pdb=" N TYR A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.609A pdb=" N THR A 183 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.513A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.810A pdb=" N ALA A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 240 through 246 removed outlier: 3.619A pdb=" N PHE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.767A pdb=" N GLU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 4.307A pdb=" N TYR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 275 through 285 removed outlier: 4.113A pdb=" N ILE A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.576A pdb=" N ALA A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.700A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.712A pdb=" N LEU A 296 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 297' Processing helix chain 'A' and resid 308 through 329 removed outlier: 3.740A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N HIS A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 325 " --> pdb=" O HIS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 341 removed outlier: 3.564A pdb=" N VAL A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 341 " --> pdb=" O TRP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.951A pdb=" N VAL A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.589A pdb=" N ILE A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.793A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.521A pdb=" N ALA A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N HIS A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.984A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.909A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 removed outlier: 3.579A pdb=" N SER A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 288 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: 0.76 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 527 1.32 - 1.44: 1086 1.44 - 1.57: 1841 1.57 - 1.69: 1 1.69 - 1.82: 31 Bond restraints: 3486 Sorted by residual: bond pdb=" CA GLN A 220 " pdb=" CB GLN A 220 " ideal model delta sigma weight residual 1.530 1.460 0.069 1.55e-02 4.16e+03 2.00e+01 bond pdb=" CA HIS A 257 " pdb=" C HIS A 257 " ideal model delta sigma weight residual 1.522 1.585 -0.063 1.43e-02 4.89e+03 1.94e+01 bond pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 1.520 1.459 0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" C GLN A 62 " pdb=" N VAL A 63 " ideal model delta sigma weight residual 1.334 1.291 0.043 1.09e-02 8.42e+03 1.59e+01 bond pdb=" CA LYS A 116 " pdb=" C LYS A 116 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.34e-02 5.57e+03 1.44e+01 ... (remaining 3481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 4699 4.35 - 8.70: 51 8.70 - 13.05: 3 13.05 - 17.40: 3 17.40 - 21.75: 2 Bond angle restraints: 4758 Sorted by residual: angle pdb=" N GLN A 220 " pdb=" CA GLN A 220 " pdb=" C GLN A 220 " ideal model delta sigma weight residual 110.32 88.57 21.75 1.59e+00 3.96e-01 1.87e+02 angle pdb=" C PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta sigma weight residual 109.35 92.11 17.24 1.98e+00 2.55e-01 7.58e+01 angle pdb=" N ALA A 221 " pdb=" CA ALA A 221 " pdb=" C ALA A 221 " ideal model delta sigma weight residual 111.34 98.94 12.40 1.49e+00 4.50e-01 6.93e+01 angle pdb=" N LYS A 116 " pdb=" CA LYS A 116 " pdb=" C LYS A 116 " ideal model delta sigma weight residual 110.80 93.20 17.60 2.13e+00 2.20e-01 6.83e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 109.24 122.13 -12.89 1.67e+00 3.59e-01 5.96e+01 ... (remaining 4753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 1776 13.82 - 27.64: 142 27.64 - 41.46: 26 41.46 - 55.28: 3 55.28 - 69.09: 2 Dihedral angle restraints: 1949 sinusoidal: 718 harmonic: 1231 Sorted by residual: dihedral pdb=" N GLN A 220 " pdb=" C GLN A 220 " pdb=" CA GLN A 220 " pdb=" CB GLN A 220 " ideal model delta harmonic sigma weight residual 122.80 105.69 17.11 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" C PHE A 115 " pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta harmonic sigma weight residual -122.60 -106.23 -16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" N LYS A 116 " pdb=" C LYS A 116 " pdb=" CA LYS A 116 " pdb=" CB LYS A 116 " ideal model delta harmonic sigma weight residual 122.80 107.35 15.45 0 2.50e+00 1.60e-01 3.82e+01 ... (remaining 1946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 368 0.057 - 0.114: 137 0.114 - 0.171: 17 0.171 - 0.228: 4 0.228 - 0.285: 3 Chirality restraints: 529 Sorted by residual: chirality pdb=" CA ASN A 117 " pdb=" N ASN A 117 " pdb=" C ASN A 117 " pdb=" CB ASN A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA LYS A 116 " pdb=" N LYS A 116 " pdb=" C LYS A 116 " pdb=" CB LYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA GLN A 220 " pdb=" N GLN A 220 " pdb=" C GLN A 220 " pdb=" CB GLN A 220 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 526 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 117 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ASN A 117 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN A 117 " -0.027 2.00e-02 2.50e+03 pdb=" N HIS A 118 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 375 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 248 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C GLY A 248 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY A 248 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A 249 " 0.022 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 845 2.78 - 3.31: 2866 3.31 - 3.84: 5249 3.84 - 4.37: 6123 4.37 - 4.90: 10226 Nonbonded interactions: 25309 Sorted by model distance: nonbonded pdb=" O TYR A 401 " pdb=" OH TYR A 425 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 227 " pdb=" OD2 ASP A 293 " model vdw 2.293 3.040 nonbonded pdb=" OG SER A 215 " pdb=" O ALA A 286 " model vdw 2.313 3.040 nonbonded pdb=" N GLN A 220 " pdb=" O GLN A 220 " model vdw 2.337 2.496 nonbonded pdb=" O TYR A 193 " pdb=" OG SER A 197 " model vdw 2.355 3.040 ... (remaining 25304 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=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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.008 0.069 3486 Z= 0.412 Angle : 1.249 21.752 4758 Z= 0.722 Chirality : 0.060 0.285 529 Planarity : 0.010 0.101 573 Dihedral : 11.080 69.094 1161 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.29 % Allowed : 4.00 % Favored : 95.71 % Cbeta Deviations : 1.27 % 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: -6.89 (0.23), residues: 418 helix: -4.63 (0.12), residues: 275 sheet: None (None), residues: 0 loop : -4.02 (0.41), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 196 HIS 0.007 0.002 HIS A 249 PHE 0.021 0.003 PHE A 335 TYR 0.026 0.003 TYR A 175 ARG 0.006 0.001 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.35368 ( 98) hydrogen bonds : angle 10.85307 ( 288) covalent geometry : bond 0.00815 ( 3486) covalent geometry : angle 1.24870 ( 4758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.325 Fit side-chains REVERT: A 85 PHE cc_start: 0.8316 (t80) cc_final: 0.8035 (t80) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1654 time to fit residues: 15.4915 Evaluate side-chains 46 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.201207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.174107 restraints weight = 4663.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178641 restraints weight = 2612.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.181652 restraints weight = 1786.091| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3486 Z= 0.146 Angle : 0.629 5.284 4758 Z= 0.336 Chirality : 0.044 0.264 529 Planarity : 0.007 0.079 573 Dihedral : 6.517 22.605 454 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.00 % Allowed : 8.29 % Favored : 89.71 % 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: -5.44 (0.31), residues: 418 helix: -3.67 (0.20), residues: 271 sheet: None (None), residues: 0 loop : -3.10 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 445 HIS 0.002 0.001 HIS A 218 PHE 0.014 0.001 PHE A 302 TYR 0.012 0.001 TYR A 175 ARG 0.004 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 98) hydrogen bonds : angle 6.00915 ( 288) covalent geometry : bond 0.00335 ( 3486) covalent geometry : angle 0.62908 ( 4758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.330 Fit side-chains REVERT: A 271 MET cc_start: 0.5595 (ttt) cc_final: 0.4965 (mtt) REVERT: A 318 MET cc_start: 0.6352 (ttt) cc_final: 0.6148 (ttt) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.1610 time to fit residues: 10.8929 Evaluate side-chains 50 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.202668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175307 restraints weight = 4582.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.179911 restraints weight = 2559.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.182961 restraints weight = 1743.432| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3486 Z= 0.125 Angle : 0.575 7.072 4758 Z= 0.301 Chirality : 0.041 0.130 529 Planarity : 0.006 0.070 573 Dihedral : 5.929 23.421 454 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.71 % Allowed : 10.86 % Favored : 87.43 % 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: -4.80 (0.33), residues: 418 helix: -3.06 (0.23), residues: 274 sheet: None (None), residues: 0 loop : -3.08 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 445 HIS 0.002 0.000 HIS A 218 PHE 0.009 0.001 PHE A 302 TYR 0.011 0.001 TYR A 465 ARG 0.007 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 98) hydrogen bonds : angle 5.43759 ( 288) covalent geometry : bond 0.00288 ( 3486) covalent geometry : angle 0.57493 ( 4758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.349 Fit side-chains REVERT: A 62 GLN cc_start: 0.7328 (pm20) cc_final: 0.7071 (pm20) REVERT: A 271 MET cc_start: 0.5325 (ttt) cc_final: 0.4677 (mtt) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.1562 time to fit residues: 9.1927 Evaluate side-chains 45 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 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 = 0.4322 r_free = 0.4322 target = 0.203561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.176169 restraints weight = 4675.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.180802 restraints weight = 2594.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.183800 restraints weight = 1766.652| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3486 Z= 0.108 Angle : 0.541 5.991 4758 Z= 0.279 Chirality : 0.040 0.145 529 Planarity : 0.005 0.066 573 Dihedral : 5.433 22.926 453 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.86 % Allowed : 11.71 % Favored : 85.43 % 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: -4.25 (0.35), residues: 418 helix: -2.61 (0.26), residues: 277 sheet: None (None), residues: 0 loop : -2.90 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 445 HIS 0.001 0.000 HIS A 218 PHE 0.008 0.001 PHE A 302 TYR 0.009 0.001 TYR A 465 ARG 0.006 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 98) hydrogen bonds : angle 4.98604 ( 288) covalent geometry : bond 0.00253 ( 3486) covalent geometry : angle 0.54142 ( 4758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.359 Fit side-chains REVERT: A 148 PHE cc_start: 0.7955 (m-80) cc_final: 0.7532 (m-80) REVERT: A 271 MET cc_start: 0.5377 (ttt) cc_final: 0.4662 (mtt) REVERT: A 322 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7165 (mm-40) REVERT: A 335 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6208 (p90) outliers start: 10 outliers final: 5 residues processed: 54 average time/residue: 0.1564 time to fit residues: 10.5607 Evaluate side-chains 48 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 37 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.207354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.178846 restraints weight = 4602.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183515 restraints weight = 2581.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.186575 restraints weight = 1772.956| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3486 Z= 0.089 Angle : 0.511 5.757 4758 Z= 0.260 Chirality : 0.040 0.131 529 Planarity : 0.005 0.061 573 Dihedral : 5.075 22.826 453 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.86 % Allowed : 14.86 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.36), residues: 418 helix: -2.24 (0.27), residues: 278 sheet: None (None), residues: 0 loop : -2.83 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 445 HIS 0.002 0.000 HIS A 218 PHE 0.006 0.001 PHE A 302 TYR 0.011 0.001 TYR A 86 ARG 0.007 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02468 ( 98) hydrogen bonds : angle 4.67485 ( 288) covalent geometry : bond 0.00203 ( 3486) covalent geometry : angle 0.51128 ( 4758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.317 Fit side-chains REVERT: A 148 PHE cc_start: 0.7919 (m-80) cc_final: 0.7507 (m-80) REVERT: A 271 MET cc_start: 0.5274 (ttt) cc_final: 0.4655 (mtt) REVERT: A 335 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.6164 (p90) outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.1516 time to fit residues: 8.9483 Evaluate side-chains 44 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.2980 chunk 27 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.206616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178214 restraints weight = 4737.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182878 restraints weight = 2630.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.185961 restraints weight = 1798.443| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3486 Z= 0.092 Angle : 0.501 5.657 4758 Z= 0.256 Chirality : 0.040 0.131 529 Planarity : 0.005 0.060 573 Dihedral : 4.920 22.884 453 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.43 % Allowed : 15.71 % Favored : 82.86 % 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: -3.51 (0.37), residues: 418 helix: -2.00 (0.28), residues: 279 sheet: None (None), residues: 0 loop : -2.72 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.001 0.000 HIS A 218 PHE 0.006 0.001 PHE A 335 TYR 0.008 0.001 TYR A 465 ARG 0.006 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02452 ( 98) hydrogen bonds : angle 4.51517 ( 288) covalent geometry : bond 0.00219 ( 3486) covalent geometry : angle 0.50130 ( 4758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.358 Fit side-chains REVERT: A 148 PHE cc_start: 0.8011 (m-80) cc_final: 0.7561 (m-80) REVERT: A 335 PHE cc_start: 0.6532 (OUTLIER) cc_final: 0.6176 (p90) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.1661 time to fit residues: 9.6320 Evaluate side-chains 45 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.204899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.176503 restraints weight = 4646.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181146 restraints weight = 2597.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184238 restraints weight = 1777.539| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3486 Z= 0.107 Angle : 0.519 5.170 4758 Z= 0.267 Chirality : 0.041 0.152 529 Planarity : 0.005 0.062 573 Dihedral : 5.008 23.275 453 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.00 % Allowed : 15.43 % Favored : 82.57 % 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: -3.32 (0.37), residues: 418 helix: -1.87 (0.28), residues: 283 sheet: None (None), residues: 0 loop : -2.61 (0.50), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.002 0.000 HIS A 218 PHE 0.007 0.001 PHE A 416 TYR 0.009 0.001 TYR A 465 ARG 0.007 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02522 ( 98) hydrogen bonds : angle 4.55534 ( 288) covalent geometry : bond 0.00254 ( 3486) covalent geometry : angle 0.51940 ( 4758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.320 Fit side-chains REVERT: A 148 PHE cc_start: 0.8023 (m-80) cc_final: 0.7571 (m-80) REVERT: A 335 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6311 (p90) outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 0.1503 time to fit residues: 9.4142 Evaluate side-chains 48 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.203541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.175028 restraints weight = 4433.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.179239 restraints weight = 2575.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.182004 restraints weight = 1789.942| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3486 Z= 0.196 Angle : 0.617 5.391 4758 Z= 0.322 Chirality : 0.045 0.142 529 Planarity : 0.005 0.069 573 Dihedral : 5.673 24.142 453 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.00 % Allowed : 15.71 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.38), residues: 418 helix: -1.94 (0.28), residues: 279 sheet: None (None), residues: 0 loop : -2.41 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 445 HIS 0.003 0.001 HIS A 218 PHE 0.011 0.002 PHE A 326 TYR 0.014 0.002 TYR A 175 ARG 0.008 0.001 ARG A 352 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 98) hydrogen bonds : angle 5.10862 ( 288) covalent geometry : bond 0.00464 ( 3486) covalent geometry : angle 0.61668 ( 4758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.319 Fit side-chains REVERT: A 271 MET cc_start: 0.5263 (ttt) cc_final: 0.4740 (tpp) REVERT: A 335 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.6308 (p90) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1517 time to fit residues: 9.8554 Evaluate side-chains 48 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.1980 chunk 32 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.207079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178142 restraints weight = 4409.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.182382 restraints weight = 2587.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.185296 restraints weight = 1809.009| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3486 Z= 0.120 Angle : 0.555 7.642 4758 Z= 0.284 Chirality : 0.042 0.164 529 Planarity : 0.005 0.060 573 Dihedral : 5.361 24.364 453 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.71 % Allowed : 16.57 % Favored : 81.71 % 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: -3.10 (0.38), residues: 418 helix: -1.69 (0.29), residues: 278 sheet: None (None), residues: 0 loop : -2.56 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 445 HIS 0.002 0.001 HIS A 167 PHE 0.016 0.001 PHE A 177 TYR 0.010 0.001 TYR A 465 ARG 0.008 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 98) hydrogen bonds : angle 4.83765 ( 288) covalent geometry : bond 0.00287 ( 3486) covalent geometry : angle 0.55527 ( 4758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.313 Fit side-chains REVERT: A 271 MET cc_start: 0.5212 (ttt) cc_final: 0.4707 (tpp) REVERT: A 335 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6276 (p90) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.1455 time to fit residues: 8.4112 Evaluate side-chains 42 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.207738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178202 restraints weight = 4415.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.182539 restraints weight = 2526.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.185616 restraints weight = 1752.961| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3486 Z= 0.114 Angle : 0.549 7.947 4758 Z= 0.281 Chirality : 0.042 0.173 529 Planarity : 0.005 0.063 573 Dihedral : 5.256 23.848 453 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 16.29 % Favored : 82.00 % 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: -2.98 (0.38), residues: 418 helix: -1.61 (0.29), residues: 280 sheet: None (None), residues: 0 loop : -2.48 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 445 HIS 0.002 0.000 HIS A 218 PHE 0.014 0.001 PHE A 177 TYR 0.010 0.001 TYR A 465 ARG 0.008 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 98) hydrogen bonds : angle 4.76419 ( 288) covalent geometry : bond 0.00273 ( 3486) covalent geometry : angle 0.54917 ( 4758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.355 Fit side-chains REVERT: A 148 PHE cc_start: 0.8030 (m-80) cc_final: 0.7508 (m-80) REVERT: A 271 MET cc_start: 0.5087 (ttt) cc_final: 0.4652 (tpp) REVERT: A 335 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.6329 (p90) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1746 time to fit residues: 9.5709 Evaluate side-chains 44 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.0070 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 0.4980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.212515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183095 restraints weight = 4398.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.187513 restraints weight = 2550.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.190565 restraints weight = 1770.329| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3486 Z= 0.089 Angle : 0.518 7.824 4758 Z= 0.265 Chirality : 0.041 0.165 529 Planarity : 0.004 0.057 573 Dihedral : 4.905 23.407 453 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.14 % Allowed : 16.29 % Favored : 82.57 % 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: -2.65 (0.39), residues: 418 helix: -1.39 (0.30), residues: 274 sheet: None (None), residues: 0 loop : -2.25 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.001 0.000 HIS A 218 PHE 0.010 0.001 PHE A 417 TYR 0.007 0.001 TYR A 465 ARG 0.008 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.02235 ( 98) hydrogen bonds : angle 4.59039 ( 288) covalent geometry : bond 0.00208 ( 3486) covalent geometry : angle 0.51768 ( 4758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.91 seconds wall clock time: 27 minutes 35.67 seconds (1655.67 seconds total)