Starting phenix.real_space_refine on Tue Sep 24 10:39:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/09_2024/7r9m_24329.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/09_2024/7r9m_24329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/09_2024/7r9m_24329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/09_2024/7r9m_24329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/09_2024/7r9m_24329.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9m_24329/09_2024/7r9m_24329.cif" } resolution = 4.0 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 3 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: 4.18, per 1000 atoms: 0.54 Number of scatterers: 7727 At special positions: 0 Unit cell: (82.08, 74.52, 103.68, 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: 1.98 Conformation dependent library (CDL) restraints added in 673.4 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 53.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'J' and resid 20 through 34 removed outlier: 3.557A pdb=" N ASN J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE J 25 " --> pdb=" O GLN J 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA J 32 " --> pdb=" O GLY J 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 68 removed outlier: 3.604A pdb=" N ARG J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 89 removed outlier: 3.851A pdb=" N ILE J 79 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 81 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN J 85 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 112 removed outlier: 3.513A pdb=" N VAL J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU J 102 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU J 109 " --> pdb=" O ARG J 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 139 removed outlier: 3.829A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY J 123 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 159 removed outlier: 3.694A pdb=" N LYS J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE J 153 " --> pdb=" O ILE J 149 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 159 " --> pdb=" O MET J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 166 through 180 removed outlier: 3.709A pdb=" N GLU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL J 175 " --> pdb=" O ALA J 171 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER J 179 " --> pdb=" O VAL J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 206 removed outlier: 3.588A pdb=" N ASP J 205 " --> pdb=" O SER J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 279 removed outlier: 4.468A pdb=" N GLU J 260 " --> pdb=" O ALA J 256 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE J 262 " --> pdb=" O LEU J 258 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS J 267 " --> pdb=" O GLU J 263 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET J 268 " --> pdb=" O GLN J 264 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE J 276 " --> pdb=" O MET J 272 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 300 removed outlier: 3.735A pdb=" N TYR J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 321 removed outlier: 3.892A pdb=" N LYS J 316 " --> pdb=" O SER J 312 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA J 318 " --> pdb=" O MET J 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS J 319 " --> pdb=" O GLU J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 398 removed outlier: 3.627A pdb=" N ILE J 377 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU J 378 " --> pdb=" O GLU J 374 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU J 379 " --> pdb=" O HIS J 375 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL J 380 " --> pdb=" O VAL J 376 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP J 386 " --> pdb=" O ARG J 382 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR J 394 " --> pdb=" O VAL J 390 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE J 395 " --> pdb=" O VAL J 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU J 396 " --> pdb=" O GLY J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 420 removed outlier: 3.868A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG J 416 " --> pdb=" O SER J 412 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU J 417 " --> pdb=" O MET J 413 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU J 420 " --> pdb=" O ARG J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 437 removed outlier: 3.653A pdb=" N VAL J 430 " --> pdb=" O GLU J 426 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU J 437 " --> pdb=" O PHE J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 449 removed outlier: 3.589A pdb=" N LEU J 444 " --> pdb=" O ILE J 440 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA J 445 " --> pdb=" O PRO J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 463 removed outlier: 3.840A pdb=" N VAL J 457 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA J 461 " --> pdb=" O VAL J 457 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS J 463 " --> pdb=" O VAL J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 487 removed outlier: 3.578A pdb=" N ASN J 486 " --> pdb=" O ASP J 482 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 511 removed outlier: 4.156A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) removed outlier: 4.084A 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: 3.590A 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 197 removed outlier: 6.897A pdb=" N LYS J 194 " --> pdb=" O MET J 367 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE J 369 " --> pdb=" O LYS J 194 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU J 196 " --> pdb=" O ILE J 369 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU J 368 " --> pdb=" O GLU J 207 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU J 207 " --> pdb=" O LEU J 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 213 through 214 removed outlier: 4.026A pdb=" N VAL J 214 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE J 354 " --> pdb=" O VAL J 214 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL J 343 " --> pdb=" O VAL J 227 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL J 227 " --> pdb=" O VAL J 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 281 through 283 removed outlier: 8.012A pdb=" N LYS J 231 " --> pdb=" O ASN J 282 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 357 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: 2.24 Time building geometry restraints manager: 2.38 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=" CA ALA J 248 " pdb=" C ALA J 248 " ideal model delta sigma weight residual 1.529 1.522 0.007 1.04e-02 9.25e+03 4.87e-01 bond pdb=" N GLU J 71 " pdb=" CA GLU J 71 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.24e-02 6.50e+03 4.68e-01 bond pdb=" N ILE J 455 " pdb=" CA ILE J 455 " ideal model delta sigma weight residual 1.452 1.459 -0.007 1.18e-02 7.18e+03 3.44e-01 bond pdb=" CA ILE J 193 " pdb=" CB ILE J 193 " ideal model delta sigma weight residual 1.540 1.532 0.008 1.36e-02 5.41e+03 3.24e-01 bond pdb=" C VAL J 212 " pdb=" O VAL J 212 " ideal model delta sigma weight residual 1.236 1.230 0.007 1.19e-02 7.06e+03 3.16e-01 ... (remaining 7743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 12647 0.78 - 1.55: 1438 1.55 - 2.33: 44 2.33 - 3.10: 11 3.10 - 3.88: 7 Bond angle restraints: 14147 Sorted by residual: angle pdb=" N ILE J 455 " pdb=" CA ILE J 455 " pdb=" C ILE J 455 " ideal model delta sigma weight residual 112.96 109.58 3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" N ILE J 440 " pdb=" CA ILE J 440 " pdb=" C ILE J 440 " ideal model delta sigma weight residual 112.35 109.29 3.06 1.20e+00 6.94e-01 6.50e+00 angle pdb=" C VAL J 439 " pdb=" N ILE J 440 " pdb=" CA ILE J 440 " ideal model delta sigma weight residual 120.33 122.13 -1.80 8.00e-01 1.56e+00 5.04e+00 angle pdb=" N GLN J 145 " pdb=" CA GLN J 145 " pdb=" C GLN J 145 " ideal model delta sigma weight residual 114.12 111.13 2.99 1.39e+00 5.18e-01 4.64e+00 angle pdb=" C ILE J 440 " pdb=" CA ILE J 440 " pdb=" CB ILE J 440 " ideal model delta sigma weight residual 114.00 111.38 2.62 1.31e+00 5.83e-01 3.99e+00 ... (remaining 14142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 3348 11.82 - 23.63: 108 23.63 - 35.45: 38 35.45 - 47.26: 22 47.26 - 59.08: 21 Dihedral angle restraints: 3537 sinusoidal: 2036 harmonic: 1501 Sorted by residual: dihedral pdb=" CB MET J 259 " pdb=" CG MET J 259 " pdb=" SD MET J 259 " pdb=" CE MET J 259 " ideal model delta sinusoidal sigma weight residual -60.00 -90.97 30.97 3 1.50e+01 4.44e-03 4.98e+00 dihedral pdb=" N LEU J 26 " pdb=" CA LEU J 26 " pdb=" CB LEU J 26 " pdb=" CG LEU J 26 " ideal model delta sinusoidal sigma weight residual -60.00 -90.40 30.40 3 1.50e+01 4.44e-03 4.84e+00 dihedral pdb=" CB MET J 272 " pdb=" CG MET J 272 " pdb=" SD MET J 272 " pdb=" CE MET J 272 " ideal model delta sinusoidal sigma weight residual -60.00 -89.94 29.94 3 1.50e+01 4.44e-03 4.73e+00 ... (remaining 3534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 395 0.025 - 0.050: 141 0.050 - 0.074: 42 0.074 - 0.099: 25 0.099 - 0.124: 27 Chirality restraints: 630 Sorted by residual: 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 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE J 193 " pdb=" N ILE J 193 " pdb=" C ILE J 193 " pdb=" CB ILE J 193 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE J 290 " pdb=" N ILE J 290 " pdb=" C ILE J 290 " pdb=" CB ILE J 290 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 627 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 254 " -0.010 5.00e-02 4.00e+02 1.53e-02 3.76e-01 pdb=" N PRO J 255 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " -0.008 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 GLY J 40 " 0.007 5.00e-02 4.00e+02 1.12e-02 2.01e-01 pdb=" N PRO J 41 " -0.019 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.006 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.006 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 116 " 0.007 5.00e-02 4.00e+02 1.05e-02 1.77e-01 pdb=" N PRO J 117 " -0.018 5.00e-02 4.00e+02 pdb=" CA PRO J 117 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO J 117 " 0.006 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 535 2.24 - 2.83: 17868 2.83 - 3.42: 17908 3.42 - 4.01: 23056 4.01 - 4.60: 36280 Nonbonded interactions: 95647 Sorted by model distance: nonbonded pdb=" OE1 GLU J 148 " pdb=" H GLU J 148 " model vdw 1.645 2.450 nonbonded pdb=" OE1 GLU J 245 " pdb=" H GLU J 245 " model vdw 1.656 2.450 nonbonded pdb=" OE1 GLU J 168 " pdb=" H GLU J 168 " model vdw 1.679 2.450 nonbonded pdb=" OE1 GLU J 263 " pdb=" H GLU J 263 " model vdw 1.696 2.450 nonbonded pdb=" OE1 GLU J 33 " pdb=" HE ARG J 36 " model vdw 1.701 2.450 ... (remaining 95642 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: 1.090 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.910 Find NCS groups from input model: 0.040 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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= 0.103 Angle : 0.380 3.877 5126 Z= 0.234 Chirality : 0.038 0.124 630 Planarity : 0.001 0.015 663 Dihedral : 4.685 38.566 1463 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.35 % Favored : 90.85 % 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: -4.83 (0.28), residues: 503 helix: -3.89 (0.21), residues: 196 sheet: -3.74 (0.49), residues: 55 loop : -2.39 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 361 PHE 0.001 0.000 PHE J 285 TYR 0.002 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 43 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 114 ASN cc_start: 0.8773 (m-40) cc_final: 0.8550 (t0) REVERT: J 155 MET cc_start: 0.9443 (mtp) cc_final: 0.8664 (tpp) REVERT: J 504 GLU cc_start: 0.9322 (tt0) cc_final: 0.9092 (pp20) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.3447 time to fit residues: 18.8888 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 0.5980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 447 ASN J 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3809 Z= 0.273 Angle : 0.586 4.426 5126 Z= 0.328 Chirality : 0.042 0.131 630 Planarity : 0.003 0.025 663 Dihedral : 2.735 11.543 529 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.25 % Allowed : 4.67 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.32), residues: 503 helix: -2.02 (0.28), residues: 219 sheet: -2.72 (0.69), residues: 46 loop : -2.31 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 296 PHE 0.009 0.001 PHE J 433 TYR 0.016 0.003 TYR J 124 ARG 0.003 0.000 ARG J 22 *********************** 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 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 155 MET cc_start: 0.9493 (mtp) cc_final: 0.8734 (tpp) REVERT: J 504 GLU cc_start: 0.9325 (tt0) cc_final: 0.9029 (tm-30) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.3284 time to fit residues: 11.2908 Evaluate side-chains 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3809 Z= 0.160 Angle : 0.446 3.808 5126 Z= 0.241 Chirality : 0.039 0.126 630 Planarity : 0.003 0.026 663 Dihedral : 2.510 12.704 529 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.98 % Allowed : 5.16 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.34), residues: 503 helix: -0.84 (0.32), residues: 224 sheet: -2.47 (0.70), residues: 46 loop : -2.00 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 463 PHE 0.004 0.001 PHE J 355 TYR 0.007 0.001 TYR J 124 ARG 0.001 0.000 ARG J 22 *********************** 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 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 155 MET cc_start: 0.9464 (mtp) cc_final: 0.8740 (tpp) REVERT: J 504 GLU cc_start: 0.9338 (tt0) cc_final: 0.9083 (tm-30) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.3543 time to fit residues: 12.1508 Evaluate side-chains 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.3816 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= 0.149 Angle : 0.439 4.937 5126 Z= 0.233 Chirality : 0.039 0.129 630 Planarity : 0.003 0.027 663 Dihedral : 2.556 13.613 529 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.74 % Allowed : 5.65 % Favored : 93.61 % 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: -1.70 (0.35), residues: 503 helix: -0.24 (0.33), residues: 225 sheet: -2.62 (0.79), residues: 32 loop : -1.75 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 296 PHE 0.003 0.001 PHE J 355 TYR 0.007 0.001 TYR J 124 ARG 0.002 0.000 ARG J 22 *********************** 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 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 504 GLU cc_start: 0.9334 (tt0) cc_final: 0.9098 (tm-30) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.3331 time to fit residues: 11.5782 Evaluate side-chains 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.4135 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= 0.150 Angle : 0.432 5.647 5126 Z= 0.228 Chirality : 0.039 0.125 630 Planarity : 0.002 0.025 663 Dihedral : 2.507 13.374 529 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.98 % Allowed : 5.65 % Favored : 93.37 % 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: -1.38 (0.35), residues: 503 helix: 0.11 (0.33), residues: 228 sheet: -2.32 (0.83), residues: 32 loop : -1.72 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.004 0.001 PHE J 355 TYR 0.006 0.001 TYR J 124 ARG 0.001 0.000 ARG J 22 *********************** 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 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 504 GLU cc_start: 0.9355 (tt0) cc_final: 0.9139 (tm-30) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.3290 time to fit residues: 11.8725 Evaluate side-chains 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 191 ASP Chi-restraints excluded: chain J residue 375 HIS 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: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.4452 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= 0.160 Angle : 0.435 4.723 5126 Z= 0.229 Chirality : 0.039 0.125 630 Planarity : 0.003 0.026 663 Dihedral : 2.603 15.106 529 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.49 % Allowed : 5.65 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.36), residues: 503 helix: 0.57 (0.34), residues: 222 sheet: -2.31 (0.73), residues: 42 loop : -1.47 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 72 PHE 0.004 0.001 PHE J 355 TYR 0.007 0.001 TYR J 124 ARG 0.002 0.000 ARG J 22 *********************** 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 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 504 GLU cc_start: 0.9365 (tt0) cc_final: 0.9119 (tm-30) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.3507 time to fit residues: 11.6310 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.4551 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= 0.121 Angle : 0.405 5.743 5126 Z= 0.211 Chirality : 0.039 0.128 630 Planarity : 0.002 0.026 663 Dihedral : 2.521 15.128 529 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.49 % Allowed : 5.16 % Favored : 94.35 % 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: -0.83 (0.36), residues: 503 helix: 0.65 (0.34), residues: 228 sheet: -2.00 (0.87), residues: 32 loop : -1.52 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 296 PHE 0.004 0.001 PHE J 355 TYR 0.006 0.001 TYR J 124 ARG 0.001 0.000 ARG J 22 *********************** 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 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 367 MET cc_start: 0.8595 (mtt) cc_final: 0.7751 (ppp) REVERT: J 504 GLU cc_start: 0.9360 (tt0) cc_final: 0.9063 (tm-30) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.3398 time to fit residues: 11.1999 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.4674 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= 0.113 Angle : 0.399 5.733 5126 Z= 0.207 Chirality : 0.038 0.125 630 Planarity : 0.002 0.025 663 Dihedral : 2.490 14.049 529 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.49 % Allowed : 5.65 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.37), residues: 503 helix: 0.96 (0.34), residues: 227 sheet: -1.90 (0.88), residues: 32 loop : -1.43 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.004 0.000 PHE J 355 TYR 0.005 0.001 TYR J 124 ARG 0.001 0.000 ARG J 442 *********************** 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 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 367 MET cc_start: 0.8556 (mtt) cc_final: 0.7796 (ppp) REVERT: J 504 GLU cc_start: 0.9363 (tt0) cc_final: 0.9087 (tm-30) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.3251 time to fit residues: 10.9784 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.4751 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= 0.101 Angle : 0.393 6.128 5126 Z= 0.202 Chirality : 0.038 0.125 630 Planarity : 0.002 0.025 663 Dihedral : 2.455 13.574 529 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.49 % Allowed : 5.41 % Favored : 94.10 % 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: -0.41 (0.37), residues: 503 helix: 1.09 (0.34), residues: 227 sheet: -1.78 (0.90), residues: 32 loop : -1.40 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.003 0.000 PHE J 355 TYR 0.004 0.001 TYR J 124 ARG 0.001 0.000 ARG J 22 *********************** 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 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 367 MET cc_start: 0.8467 (mtt) cc_final: 0.7766 (ppp) REVERT: J 504 GLU cc_start: 0.9359 (tt0) cc_final: 0.9083 (tm-30) outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.3399 time to fit residues: 11.3117 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.4964 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= 0.144 Angle : 0.412 5.753 5126 Z= 0.218 Chirality : 0.038 0.125 630 Planarity : 0.002 0.027 663 Dihedral : 2.539 12.900 529 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.10 % 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: -0.40 (0.37), residues: 503 helix: 1.12 (0.34), residues: 228 sheet: -1.79 (0.90), residues: 32 loop : -1.42 (0.38), residues: 243 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 0.008 0.001 TYR J 124 ARG 0.002 0.000 ARG J 105 ********************** 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 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 155 MET cc_start: 0.9467 (mtp) cc_final: 0.8899 (tpp) REVERT: J 367 MET cc_start: 0.8515 (mtt) cc_final: 0.7809 (ppp) REVERT: J 504 GLU cc_start: 0.9376 (tt0) cc_final: 0.9131 (tm-30) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.3488 time to fit residues: 11.8340 Evaluate side-chains 24 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0010 chunk 5 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 0.2084 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.061832 restraints weight = 58065.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063330 restraints weight = 24200.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064213 restraints weight = 14716.319| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5001 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= 0.103 Angle : 0.403 6.083 5126 Z= 0.204 Chirality : 0.038 0.126 630 Planarity : 0.002 0.024 663 Dihedral : 2.480 13.321 529 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.25 % Allowed : 5.90 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.37), residues: 503 helix: 1.23 (0.34), residues: 227 sheet: -1.74 (0.90), residues: 32 loop : -1.34 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.004 0.000 PHE J 355 TYR 0.004 0.001 TYR J 124 ARG 0.001 0.000 ARG J 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.69 seconds wall clock time: 43 minutes 15.09 seconds (2595.09 seconds total)