Starting phenix.real_space_refine on Tue Sep 24 09:46:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/09_2024/7r9u_24331.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/09_2024/7r9u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/09_2024/7r9u_24331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/09_2024/7r9u_24331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/09_2024/7r9u_24331.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9u_24331/09_2024/7r9u_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-5461/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: 4.22, per 1000 atoms: 0.55 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: 1.69 Conformation dependent library (CDL) restraints added in 661.1 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: 0.54 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: 2.19 Time building geometry restraints manager: 2.10 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: 7.370 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.700 Find NCS groups from input model: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.960 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.611 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: 0.3795 time to fit residues: 26.5792 Evaluate side-chains 32 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.611 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 473 LEU cc_start: 0.7606 (tp) cc_final: 0.7295 (tt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.3739 time to fit residues: 16.9825 Evaluate side-chains 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3809 Z= 0.164 Angle : 0.447 4.376 5126 Z= 0.246 Chirality : 0.038 0.130 630 Planarity : 0.002 0.025 663 Dihedral : 2.748 10.364 529 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.65 (0.35), residues: 503 helix: -0.49 (0.32), residues: 214 sheet: -2.34 (0.58), residues: 64 loop : -1.17 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 116 PHE 0.017 0.002 PHE J 285 TYR 0.004 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 fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.570 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: 0.7628 (tp) cc_final: 0.7317 (tt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.4211 time to fit residues: 14.3018 Evaluate side-chains 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4398 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= 0.139 Angle : 0.406 4.286 5126 Z= 0.224 Chirality : 0.038 0.128 630 Planarity : 0.002 0.023 663 Dihedral : 2.765 10.857 529 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.88 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: -0.78 (0.36), residues: 503 helix: 0.28 (0.33), residues: 218 sheet: -1.40 (0.69), residues: 55 loop : -0.98 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 375 PHE 0.014 0.002 PHE J 285 TYR 0.005 0.001 TYR J 124 ARG 0.001 0.000 ARG J 308 *********************** 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 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.638 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 473 LEU cc_start: 0.7693 (tp) cc_final: 0.7401 (tt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.4514 time to fit residues: 14.1071 Evaluate side-chains 24 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3809 Z= 0.223 Angle : 0.498 4.351 5126 Z= 0.278 Chirality : 0.038 0.131 630 Planarity : 0.003 0.031 663 Dihedral : 3.120 13.168 529 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -0.52 (0.36), residues: 503 helix: 0.49 (0.33), residues: 222 sheet: -1.13 (0.77), residues: 45 loop : -0.92 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 116 PHE 0.017 0.002 PHE J 285 TYR 0.005 0.001 TYR J 124 ARG 0.002 0.001 ARG J 460 *********************** 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 22 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.3750 time to fit residues: 10.7299 Evaluate side-chains 21 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 0.0470 chunk 16 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5391 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= 0.107 Angle : 0.382 4.106 5126 Z= 0.206 Chirality : 0.038 0.127 630 Planarity : 0.002 0.022 663 Dihedral : 2.857 10.769 529 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -0.00 (0.38), residues: 503 helix: 0.99 (0.35), residues: 220 sheet: -0.87 (0.74), residues: 55 loop : -0.69 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 72 PHE 0.006 0.001 PHE J 355 TYR 0.001 0.000 TYR J 418 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 fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.3317 time to fit residues: 10.5547 Evaluate side-chains 21 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5660 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= 0.130 Angle : 0.397 4.366 5126 Z= 0.219 Chirality : 0.038 0.126 630 Planarity : 0.002 0.023 663 Dihedral : 2.901 10.176 529 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 0.19 (0.38), residues: 503 helix: 1.08 (0.34), residues: 223 sheet: -0.67 (0.76), residues: 55 loop : -0.56 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 116 PHE 0.009 0.001 PHE J 285 TYR 0.002 0.001 TYR J 297 ARG 0.001 0.000 ARG J 308 *********************** 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 21 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.642 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 outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.3372 time to fit residues: 9.5328 Evaluate side-chains 21 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3809 Z= 0.172 Angle : 0.436 4.692 5126 Z= 0.244 Chirality : 0.038 0.125 630 Planarity : 0.003 0.027 663 Dihedral : 3.079 11.865 529 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 0.33 (0.38), residues: 503 helix: 1.15 (0.34), residues: 221 sheet: -0.52 (0.77), residues: 55 loop : -0.45 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.007 0.001 PHE J 285 TYR 0.003 0.001 TYR J 124 ARG 0.002 0.000 ARG J 511 *********************** 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 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.3597 time to fit residues: 9.6945 Evaluate side-chains 19 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.6108 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= 0.100 Angle : 0.392 4.626 5126 Z= 0.211 Chirality : 0.038 0.128 630 Planarity : 0.002 0.022 663 Dihedral : 2.889 9.523 529 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 0.58 (0.38), residues: 503 helix: 1.30 (0.35), residues: 224 sheet: -0.15 (0.89), residues: 45 loop : -0.35 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 72 PHE 0.006 0.001 PHE J 355 TYR 0.003 0.001 TYR J 418 ARG 0.001 0.000 ARG J 307 *********************** 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 22 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.3308 time to fit residues: 9.7870 Evaluate side-chains 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.6284 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= 0.125 Angle : 0.401 4.770 5126 Z= 0.220 Chirality : 0.038 0.124 630 Planarity : 0.002 0.021 663 Dihedral : 2.906 10.456 529 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: 0.54 (0.39), residues: 503 helix: 1.31 (0.35), residues: 225 sheet: -0.40 (0.78), residues: 55 loop : -0.35 (0.43), residues: 223 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 511 ********************** 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 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.2952 time to fit residues: 8.6738 Evaluate side-chains 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 overall best weight: 1.3164 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.042765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.029436 restraints weight = 110390.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.030617 restraints weight = 57993.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.031393 restraints weight = 36491.750| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3809 Z= 0.176 Angle : 0.445 5.072 5126 Z= 0.248 Chirality : 0.038 0.122 630 Planarity : 0.003 0.026 663 Dihedral : 3.133 12.175 529 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: 0.33 (0.38), residues: 503 helix: 1.16 (0.34), residues: 226 sheet: -0.39 (0.78), residues: 55 loop : -0.53 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 72 PHE 0.005 0.001 PHE J 355 TYR 0.003 0.001 TYR J 297 ARG 0.002 0.000 ARG J 511 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2494.46 seconds wall clock time: 44 minutes 12.64 seconds (2652.64 seconds total)