Starting phenix.real_space_refine on Wed Mar 12 10:16:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r9u_24331/03_2025/7r9u_24331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r9u_24331/03_2025/7r9u_24331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r9u_24331/03_2025/7r9u_24331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r9u_24331/03_2025/7r9u_24331.map" model { file = "/net/cci-nas-00/data/ceres_data/7r9u_24331/03_2025/7r9u_24331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r9u_24331/03_2025/7r9u_24331.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 23 5.16 5 C 2351 2.51 5 N 655 2.21 5 O 759 1.98 5 H 3939 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7727 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 7727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7727 Classifications: {'peptide': 505} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 496} Time building chain proxies: 4.14, per 1000 atoms: 0.54 Number of scatterers: 7727 At special positions: 0 Unit cell: (78.84, 72.36, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 O 759 8.00 N 655 7.00 C 2351 6.00 H 3939 1.00 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: 1.90 Conformation dependent library (CDL) restraints added in 712.8 milliseconds 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 51.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'J' and resid 21 through 37 removed outlier: 4.005A pdb=" N ILE J 25 " --> pdb=" O GLN J 21 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL J 35 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 68 removed outlier: 3.932A pdb=" N ILE J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 87 removed outlier: 3.643A pdb=" N THR J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN J 85 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 87 " --> pdb=" O LYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 113 removed outlier: 3.634A pdb=" N VAL J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY J 101 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU J 102 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU J 109 " --> pdb=" O ARG J 105 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 139 removed outlier: 3.674A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY J 123 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 159 removed outlier: 3.608A pdb=" N LEU J 150 " --> pdb=" O ASP J 146 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE J 153 " --> pdb=" O ILE J 149 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA J 154 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 181 removed outlier: 3.562A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA J 177 " --> pdb=" O ILE J 173 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA J 180 " --> pdb=" O GLU J 176 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 206 removed outlier: 3.826A pdb=" N ASP J 205 " --> pdb=" O SER J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 260 removed outlier: 3.711A pdb=" N MET J 259 " --> pdb=" O ALA J 256 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU J 260 " --> pdb=" O LYS J 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 256 through 260' Processing helix chain 'J' and resid 262 through 279 removed outlier: 3.787A pdb=" N GLU J 266 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU J 269 " --> pdb=" O GLU J 265 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS J 270 " --> pdb=" O GLU J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 301 removed outlier: 4.145A pdb=" N TYR J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 298 " --> pdb=" O ALA J 294 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA J 299 " --> pdb=" O GLN J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 4.255A pdb=" N LYS J 316 " --> pdb=" O SER J 312 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR J 321 " --> pdb=" O LEU J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 398 removed outlier: 3.576A pdb=" N ALA J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP J 386 " --> pdb=" O ARG J 382 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL J 388 " --> pdb=" O VAL J 384 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR J 394 " --> pdb=" O VAL J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 420 removed outlier: 3.504A pdb=" N LEU J 411 " --> pdb=" O THR J 407 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS J 414 " --> pdb=" O GLU J 410 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG J 416 " --> pdb=" O SER J 412 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU J 417 " --> pdb=" O MET J 413 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU J 420 " --> pdb=" O ARG J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 425 No H-bonds generated for 'chain 'J' and resid 423 through 425' Processing helix chain 'J' and resid 426 through 435 Processing helix chain 'J' and resid 438 through 449 removed outlier: 3.671A pdb=" N ARG J 442 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 444 " --> pdb=" O ILE J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 463 removed outlier: 3.955A pdb=" N LYS J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA J 461 " --> pdb=" O VAL J 457 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS J 463 " --> pdb=" O VAL J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 487 removed outlier: 3.560A pdb=" N GLY J 487 " --> pdb=" O MET J 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 483 through 487' Processing helix chain 'J' and resid 492 through 511 removed outlier: 3.628A pdb=" N THR J 496 " --> pdb=" O LEU J 492 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 498 " --> pdb=" O VAL J 494 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU J 509 " --> pdb=" O SER J 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 140 through 141 removed outlier: 3.760A pdb=" N ILE J 400 " --> pdb=" O CYS J 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 193 through 199 removed outlier: 6.619A pdb=" N LYS J 194 " --> pdb=" O MET J 367 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE J 369 " --> pdb=" O LYS J 194 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU J 196 " --> pdb=" O ILE J 369 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLY J 371 " --> pdb=" O GLU J 196 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS J 198 " --> pdb=" O GLY J 371 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR J 366 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE J 209 " --> pdb=" O THR J 366 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU J 368 " --> pdb=" O GLU J 207 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU J 207 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'J' and resid 212 through 214 removed outlier: 3.776A pdb=" N ARG J 346 " --> pdb=" O MET J 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 471 through 472 removed outlier: 3.503A pdb=" N GLY J 472 " --> pdb=" O GLU J 481 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU J 481 " --> pdb=" O GLY J 472 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 121 hydrogen bonds defined for protein. 351 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3932 1.03 - 1.23: 7 1.23 - 1.42: 1405 1.42 - 1.61: 2365 1.61 - 1.81: 39 Bond restraints: 7748 Sorted by residual: bond pdb=" N GLY J 200 " pdb=" CA GLY J 200 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 8.92e-01 bond pdb=" CA VAL J 219 " pdb=" C VAL J 219 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.12e-02 7.97e+03 3.91e-01 bond pdb=" CA GLY J 200 " pdb=" C GLY J 200 " ideal model delta sigma weight residual 1.504 1.514 -0.011 1.83e-02 2.99e+03 3.48e-01 bond pdb=" C GLY J 200 " pdb=" O GLY J 200 " ideal model delta sigma weight residual 1.239 1.234 0.005 8.50e-03 1.38e+04 2.97e-01 bond pdb=" N LYS J 42 " pdb=" CA LYS J 42 " ideal model delta sigma weight residual 1.464 1.457 0.006 1.20e-02 6.94e+03 2.91e-01 ... (remaining 7743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.76: 12657 0.76 - 1.52: 1432 1.52 - 2.28: 48 2.28 - 3.04: 3 3.04 - 3.80: 7 Bond angle restraints: 14147 Sorted by residual: angle pdb=" N VAL J 219 " pdb=" CA VAL J 219 " pdb=" C VAL J 219 " ideal model delta sigma weight residual 111.91 109.75 2.16 8.90e-01 1.26e+00 5.89e+00 angle pdb=" N LYS J 330 " pdb=" CA LYS J 330 " pdb=" C LYS J 330 " ideal model delta sigma weight residual 112.97 111.17 1.80 1.06e+00 8.90e-01 2.88e+00 angle pdb=" C ILE J 262 " pdb=" CA ILE J 262 " pdb=" CB ILE J 262 " ideal model delta sigma weight residual 111.65 109.45 2.20 1.41e+00 5.03e-01 2.45e+00 angle pdb=" C VAL J 62 " pdb=" CA VAL J 62 " pdb=" CB VAL J 62 " ideal model delta sigma weight residual 112.16 109.66 2.50 1.63e+00 3.76e-01 2.36e+00 angle pdb=" CA ILE J 440 " pdb=" C ILE J 440 " pdb=" N PRO J 441 " ideal model delta sigma weight residual 118.88 120.92 -2.04 1.54e+00 4.22e-01 1.75e+00 ... (remaining 14142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.86: 3339 11.86 - 23.72: 121 23.72 - 35.58: 33 35.58 - 47.44: 28 47.44 - 59.30: 16 Dihedral angle restraints: 3537 sinusoidal: 2036 harmonic: 1501 Sorted by residual: dihedral pdb=" CA LEU J 284 " pdb=" CB LEU J 284 " pdb=" CG LEU J 284 " pdb=" CD1 LEU J 284 " ideal model delta sinusoidal sigma weight residual 180.00 142.01 37.99 3 1.50e+01 4.44e-03 6.67e+00 dihedral pdb=" CB MET J 508 " pdb=" CG MET J 508 " pdb=" SD MET J 508 " pdb=" CE MET J 508 " ideal model delta sinusoidal sigma weight residual 60.00 95.72 -35.72 3 1.50e+01 4.44e-03 6.14e+00 dihedral pdb=" CB MET J 483 " pdb=" CG MET J 483 " pdb=" SD MET J 483 " pdb=" CE MET J 483 " ideal model delta sinusoidal sigma weight residual 60.00 92.54 -32.54 3 1.50e+01 4.44e-03 5.37e+00 ... (remaining 3534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 376 0.024 - 0.048: 154 0.048 - 0.072: 50 0.072 - 0.097: 18 0.097 - 0.121: 32 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA ILE J 326 " pdb=" N ILE J 326 " pdb=" C ILE J 326 " pdb=" CB ILE J 326 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE J 303 " pdb=" N ILE J 303 " pdb=" C ILE J 303 " pdb=" CB ILE J 303 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA VAL J 214 " pdb=" N VAL J 214 " pdb=" C VAL J 214 " pdb=" CB VAL J 214 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 627 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 254 " -0.011 5.00e-02 4.00e+02 1.68e-02 4.54e-01 pdb=" N PRO J 255 " 0.029 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO J 255 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 116 " 0.009 5.00e-02 4.00e+02 1.38e-02 3.03e-01 pdb=" N PRO J 117 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO J 117 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO J 117 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET J 223 " 0.006 5.00e-02 4.00e+02 9.61e-03 1.48e-01 pdb=" N PRO J 224 " -0.017 5.00e-02 4.00e+02 pdb=" CA PRO J 224 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO J 224 " 0.005 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 526 2.23 - 2.83: 17885 2.83 - 3.42: 17716 3.42 - 4.01: 22870 4.01 - 4.60: 36498 Nonbonded interactions: 95495 Sorted by model distance: nonbonded pdb=" OE1 GLU J 168 " pdb=" H GLU J 168 " model vdw 1.642 2.450 nonbonded pdb="HD21 ASN J 328 " pdb=" OD2 ASP J 331 " model vdw 1.696 2.450 nonbonded pdb=" OD1 ASP J 183 " pdb=" H LYS J 187 " model vdw 1.744 2.450 nonbonded pdb=" OE1 GLU J 172 " pdb=" H GLU J 172 " model vdw 1.749 2.450 nonbonded pdb=" O LYS J 152 " pdb=" HG1 THR J 156 " model vdw 1.757 2.450 ... (remaining 95490 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: 53.000 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: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.220 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 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 : 0.002 0.011 3809 Z= 0.100 Angle : 0.342 3.797 5126 Z= 0.205 Chirality : 0.038 0.121 630 Planarity : 0.001 0.017 663 Dihedral : 4.356 37.994 1463 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.15 % Favored : 90.26 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -4.49 (0.31), residues: 503 helix: -3.85 (0.20), residues: 184 sheet: -3.70 (0.54), residues: 57 loop : -2.04 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 72 PHE 0.001 0.000 PHE J 355 TYR 0.001 0.000 TYR J 418 ARG 0.001 0.000 ARG J 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 473 LEU cc_start: 0.7573 (tp) cc_final: 0.7188 (tt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3646 time to fit residues: 25.3667 Evaluate side-chains 32 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.046532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.032726 restraints weight = 112341.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.034042 restraints weight = 58819.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.034966 restraints weight = 36862.293| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3809 Z= 0.181 Angle : 0.508 4.839 5126 Z= 0.282 Chirality : 0.039 0.132 630 Planarity : 0.003 0.048 663 Dihedral : 2.803 10.604 529 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.98 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -2.89 (0.34), residues: 503 helix: -1.79 (0.30), residues: 217 sheet: -2.81 (0.53), residues: 68 loop : -1.53 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 375 PHE 0.013 0.002 PHE J 355 TYR 0.015 0.003 TYR J 124 ARG 0.002 0.000 ARG J 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9717 (pmm) cc_final: 0.9457 (pmm) REVERT: J 413 MET cc_start: 0.9029 (mmp) cc_final: 0.8769 (mmm) REVERT: J 473 LEU cc_start: 0.9556 (tp) cc_final: 0.9282 (tt) REVERT: J 483 MET cc_start: 0.9499 (mmp) cc_final: 0.9068 (mmm) REVERT: J 508 MET cc_start: 0.9629 (mmp) cc_final: 0.9312 (mmp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.4009 time to fit residues: 18.4293 Evaluate side-chains 28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.045819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.031895 restraints weight = 108294.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.033174 restraints weight = 57275.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034061 restraints weight = 36246.733| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3809 Z= 0.138 Angle : 0.420 4.354 5126 Z= 0.231 Chirality : 0.038 0.129 630 Planarity : 0.002 0.026 663 Dihedral : 2.661 10.073 529 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.36), residues: 503 helix: -0.63 (0.33), residues: 218 sheet: -2.40 (0.56), residues: 70 loop : -1.17 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 463 PHE 0.015 0.001 PHE J 285 TYR 0.002 0.001 TYR J 418 ARG 0.003 0.000 ARG J 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9729 (pmm) cc_final: 0.9335 (pmm) REVERT: J 413 MET cc_start: 0.9153 (mmp) cc_final: 0.8896 (mmm) REVERT: J 473 LEU cc_start: 0.9570 (tp) cc_final: 0.9315 (tt) REVERT: J 483 MET cc_start: 0.9514 (mmp) cc_final: 0.9108 (mmm) REVERT: J 508 MET cc_start: 0.9582 (mmp) cc_final: 0.9285 (mmp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.4411 time to fit residues: 15.2106 Evaluate side-chains 25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.045234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.031931 restraints weight = 104718.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033261 restraints weight = 52950.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.034145 restraints weight = 32450.540| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3809 Z= 0.123 Angle : 0.392 4.250 5126 Z= 0.213 Chirality : 0.038 0.127 630 Planarity : 0.002 0.025 663 Dihedral : 2.679 10.567 529 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -0.89 (0.36), residues: 503 helix: 0.11 (0.33), residues: 217 sheet: -1.33 (0.70), residues: 55 loop : -0.99 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 72 PHE 0.017 0.002 PHE J 285 TYR 0.005 0.001 TYR J 124 ARG 0.001 0.000 ARG J 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9752 (pmm) cc_final: 0.9324 (pmm) REVERT: J 413 MET cc_start: 0.9292 (mmp) cc_final: 0.9014 (mmm) REVERT: J 508 MET cc_start: 0.9568 (mmp) cc_final: 0.9253 (mmp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.4354 time to fit residues: 14.1036 Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.045659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031591 restraints weight = 109385.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032879 restraints weight = 57138.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033755 restraints weight = 35614.584| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3809 Z= 0.117 Angle : 0.394 4.217 5126 Z= 0.214 Chirality : 0.038 0.138 630 Planarity : 0.002 0.025 663 Dihedral : 2.629 9.590 529 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.37 (0.37), residues: 503 helix: 0.57 (0.34), residues: 217 sheet: -0.98 (0.81), residues: 45 loop : -0.79 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.014 0.001 PHE J 285 TYR 0.002 0.000 TYR J 297 ARG 0.001 0.000 ARG J 431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9750 (pmm) cc_final: 0.9347 (pmm) REVERT: J 413 MET cc_start: 0.9300 (mmp) cc_final: 0.9025 (mmm) REVERT: J 508 MET cc_start: 0.9540 (mmp) cc_final: 0.9221 (mmp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.3852 time to fit residues: 11.6416 Evaluate side-chains 22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 12 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 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 = 0.3306 r_free = 0.3306 target = 0.045250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.031323 restraints weight = 108696.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.032590 restraints weight = 56637.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.033463 restraints weight = 35457.942| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3809 Z= 0.103 Angle : 0.372 4.302 5126 Z= 0.200 Chirality : 0.038 0.126 630 Planarity : 0.002 0.024 663 Dihedral : 2.638 9.915 529 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 0.02 (0.37), residues: 503 helix: 0.89 (0.35), residues: 218 sheet: -0.62 (0.84), residues: 45 loop : -0.61 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.012 0.001 PHE J 285 TYR 0.001 0.000 TYR J 297 ARG 0.001 0.000 ARG J 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9736 (pmm) cc_final: 0.9321 (pmm) REVERT: J 413 MET cc_start: 0.9345 (mmp) cc_final: 0.9058 (mmm) REVERT: J 483 MET cc_start: 0.9512 (mmp) cc_final: 0.9026 (mmm) REVERT: J 508 MET cc_start: 0.9509 (mmp) cc_final: 0.9190 (mmp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.3728 time to fit residues: 11.2688 Evaluate side-chains 22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.045221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031389 restraints weight = 110238.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032622 restraints weight = 57071.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.033525 restraints weight = 36047.416| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3809 Z= 0.110 Angle : 0.383 4.383 5126 Z= 0.206 Chirality : 0.038 0.127 630 Planarity : 0.002 0.024 663 Dihedral : 2.628 9.175 529 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.26 (0.38), residues: 503 helix: 1.09 (0.35), residues: 218 sheet: -0.43 (0.85), residues: 45 loop : -0.50 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.011 0.001 PHE J 285 TYR 0.001 0.000 TYR J 124 ARG 0.001 0.000 ARG J 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9717 (pmm) cc_final: 0.9311 (pmm) REVERT: J 413 MET cc_start: 0.9350 (mmp) cc_final: 0.9068 (mmm) REVERT: J 483 MET cc_start: 0.9523 (mmp) cc_final: 0.9068 (mmm) REVERT: J 508 MET cc_start: 0.9494 (mmp) cc_final: 0.9158 (mmp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.3896 time to fit residues: 11.7710 Evaluate side-chains 22 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.044961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.030984 restraints weight = 113307.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.032267 restraints weight = 58731.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.033124 restraints weight = 36279.887| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3809 Z= 0.111 Angle : 0.380 4.657 5126 Z= 0.204 Chirality : 0.038 0.124 630 Planarity : 0.002 0.023 663 Dihedral : 2.653 9.622 529 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.44 (0.38), residues: 503 helix: 1.26 (0.35), residues: 217 sheet: -0.27 (0.86), residues: 45 loop : -0.43 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.007 0.001 PHE J 285 TYR 0.001 0.000 TYR J 124 ARG 0.001 0.000 ARG J 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9721 (pmm) cc_final: 0.9473 (pmm) REVERT: J 413 MET cc_start: 0.9337 (mmp) cc_final: 0.9051 (mmm) REVERT: J 483 MET cc_start: 0.9500 (mmp) cc_final: 0.9077 (mmm) REVERT: J 508 MET cc_start: 0.9446 (mmp) cc_final: 0.9070 (mmp) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.3850 time to fit residues: 12.2210 Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 6 optimal weight: 0.5980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.044593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.030837 restraints weight = 112139.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.032106 restraints weight = 57609.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.032986 restraints weight = 35686.621| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3809 Z= 0.109 Angle : 0.387 4.667 5126 Z= 0.210 Chirality : 0.038 0.125 630 Planarity : 0.002 0.023 663 Dihedral : 2.668 8.613 529 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.57 (0.38), residues: 503 helix: 1.34 (0.35), residues: 218 sheet: -0.09 (0.87), residues: 45 loop : -0.36 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.005 0.001 PHE J 355 TYR 0.001 0.000 TYR J 297 ARG 0.001 0.000 ARG J 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 155 MET cc_start: 0.9286 (tmm) cc_final: 0.9005 (tpp) REVERT: J 353 MET cc_start: 0.9742 (pmm) cc_final: 0.9520 (pmm) REVERT: J 413 MET cc_start: 0.9304 (mmp) cc_final: 0.9031 (mmm) REVERT: J 483 MET cc_start: 0.9504 (mmp) cc_final: 0.9092 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.3559 time to fit residues: 10.6594 Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.043805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.030007 restraints weight = 110937.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.031216 restraints weight = 57777.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.032045 restraints weight = 36070.752| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3809 Z= 0.128 Angle : 0.399 5.081 5126 Z= 0.217 Chirality : 0.038 0.124 630 Planarity : 0.002 0.022 663 Dihedral : 2.769 9.935 529 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.67 (0.38), residues: 503 helix: 1.36 (0.35), residues: 225 sheet: 0.15 (0.88), residues: 45 loop : -0.34 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.005 0.001 PHE J 355 TYR 0.002 0.000 TYR J 297 ARG 0.001 0.000 ARG J 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 353 MET cc_start: 0.9742 (pmm) cc_final: 0.9536 (pmm) REVERT: J 413 MET cc_start: 0.9331 (mmp) cc_final: 0.9052 (mmm) REVERT: J 483 MET cc_start: 0.9514 (mmp) cc_final: 0.9129 (mmm) REVERT: J 508 MET cc_start: 0.9355 (mmp) cc_final: 0.8797 (mmp) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.4706 time to fit residues: 14.5718 Evaluate side-chains 23 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.044265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.030338 restraints weight = 110971.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031611 restraints weight = 57368.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.032460 restraints weight = 35730.428| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3809 Z= 0.099 Angle : 0.378 4.796 5126 Z= 0.203 Chirality : 0.038 0.124 630 Planarity : 0.002 0.022 663 Dihedral : 2.707 8.367 529 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.81 (0.38), residues: 503 helix: 1.50 (0.35), residues: 224 sheet: 0.28 (0.89), residues: 45 loop : -0.30 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.005 0.001 PHE J 355 TYR 0.002 0.000 TYR J 297 ARG 0.001 0.000 ARG J 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3783.92 seconds wall clock time: 67 minutes 7.54 seconds (4027.54 seconds total)