Starting phenix.real_space_refine on Sat Apr 6 08:13:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/04_2024/7r9k_24328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/04_2024/7r9k_24328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/04_2024/7r9k_24328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/04_2024/7r9k_24328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/04_2024/7r9k_24328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9k_24328/04_2024/7r9k_24328.pdb" } resolution = 4.1 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 3938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 522": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7726 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 7726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7726 Classifications: {'peptide': 505} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 496} Time building chain proxies: 3.84, per 1000 atoms: 0.50 Number of scatterers: 7726 At special positions: 0 Unit cell: (75.6, 77.76, 104.76, 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 3938 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 - 3.50 Amino acid : False - 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: 5.87 Conformation dependent library (CDL) restraints added in 794.2 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: 19 helices and 4 sheets defined 54.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'J' and resid 20 through 35 removed outlier: 3.862A pdb=" N LEU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY J 28 " --> pdb=" O ASN J 24 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL J 35 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 66 Processing helix chain 'J' and resid 75 through 89 removed outlier: 3.896A pdb=" N ILE J 79 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL J 81 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS J 87 " --> pdb=" O LYS J 83 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU J 88 " --> pdb=" O THR J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 113 removed outlier: 3.842A pdb=" N ALA J 96 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU J 109 " --> pdb=" O ARG J 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 139 removed outlier: 3.795A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL J 121 " --> pdb=" O PRO J 117 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS J 122 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE J 138 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 162 removed outlier: 3.960A pdb=" N LYS J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS J 161 " --> pdb=" O SER J 157 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 182 removed outlier: 4.097A pdb=" N GLU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA J 180 " --> pdb=" O GLU J 176 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL J 182 " --> pdb=" O VAL J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 206 removed outlier: 3.543A pdb=" N ASP J 205 " --> pdb=" O SER J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 271 removed outlier: 3.799A pdb=" N GLU J 260 " --> pdb=" O ALA J 256 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE J 261 " --> pdb=" O LYS J 257 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE J 262 " --> pdb=" O LEU J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 279 removed outlier: 3.691A pdb=" N GLU J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 302 removed outlier: 3.989A pdb=" N HIS J 296 " --> pdb=" O ASP J 292 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.723A pdb=" N MET J 314 " --> pdb=" O LYS J 310 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU J 315 " --> pdb=" O LYS J 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA J 318 " --> pdb=" O MET J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 398 removed outlier: 4.552A pdb=" N GLU J 379 " --> pdb=" O HIS J 375 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL J 380 " --> pdb=" O VAL J 376 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG J 382 " --> pdb=" O GLU J 378 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 388 " --> pdb=" O VAL J 384 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR J 394 " --> pdb=" O VAL J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 422 removed outlier: 3.836A pdb=" N GLU J 410 " --> pdb=" O SER J 406 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU J 411 " --> pdb=" O THR J 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER J 412 " --> pdb=" O GLU J 408 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG J 416 " --> pdb=" O SER J 412 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU J 417 " --> pdb=" O MET J 413 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR J 418 " --> pdb=" O LYS J 414 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY J 421 " --> pdb=" O GLU J 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE J 422 " --> pdb=" O TYR J 418 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 438 removed outlier: 3.806A pdb=" N ALA J 429 " --> pdb=" O ARG J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 447 removed outlier: 3.559A pdb=" N THR J 443 " --> pdb=" O VAL J 439 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA J 445 " --> pdb=" O PRO J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 463 removed outlier: 3.605A pdb=" N VAL J 457 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 487 removed outlier: 3.974A pdb=" N ASN J 486 " --> pdb=" O ASP J 482 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY J 487 " --> pdb=" O MET J 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 482 through 487' Processing helix chain 'J' and resid 492 through 512 removed outlier: 3.693A pdb=" N GLN J 497 " --> pdb=" O ARG J 493 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU J 504 " --> pdb=" O GLN J 500 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 509 " --> pdb=" O SER J 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 49 removed outlier: 4.251A pdb=" N LYS J 46 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR J 58 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL J 56 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AA3, first strand: chain 'J' and resid 193 through 197 removed outlier: 7.115A pdb=" N LYS J 194 " --> pdb=" O MET J 367 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE J 369 " --> pdb=" O LYS J 194 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU J 196 " --> pdb=" O ILE J 369 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU J 368 " --> pdb=" O GLU J 207 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU J 207 " --> pdb=" O LEU J 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 226 through 228 removed outlier: 3.504A pdb=" N VAL J 227 " --> pdb=" O VAL J 343 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU J 342 " --> pdb=" O GLU J 357 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 405 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: 2.35 Time building geometry restraints manager: 6.20 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: 3931 1.03 - 1.23: 7 1.23 - 1.42: 1405 1.42 - 1.61: 2365 1.61 - 1.81: 39 Bond restraints: 7747 Sorted by residual: bond pdb=" C ILE J 239 " pdb=" N GLU J 240 " ideal model delta sigma weight residual 1.332 1.325 0.007 1.40e-02 5.10e+03 2.71e-01 bond pdb=" NE ARG J 431 " pdb=" CZ ARG J 431 " ideal model delta sigma weight residual 1.326 1.331 -0.005 1.10e-02 8.26e+03 2.33e-01 bond pdb=" C VAL J 439 " pdb=" O VAL J 439 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.19e-02 7.06e+03 2.31e-01 bond pdb=" C ILE J 440 " pdb=" N PRO J 441 " ideal model delta sigma weight residual 1.337 1.343 -0.006 1.24e-02 6.50e+03 2.25e-01 bond pdb=" CB PRO J 441 " pdb=" CG PRO J 441 " ideal model delta sigma weight residual 1.492 1.471 0.021 5.00e-02 4.00e+02 1.82e-01 ... (remaining 7742 not shown) Histogram of bond angle deviations from ideal: 100.90 - 106.98: 62 106.98 - 113.05: 9881 113.05 - 119.13: 1583 119.13 - 125.20: 2568 125.20 - 131.28: 51 Bond angle restraints: 14145 Sorted by residual: angle pdb=" CA VAL J 439 " pdb=" C VAL J 439 " pdb=" N ILE J 440 " ideal model delta sigma weight residual 116.60 119.38 -2.78 1.45e+00 4.76e-01 3.68e+00 angle pdb=" N VAL J 439 " pdb=" CA VAL J 439 " pdb=" C VAL J 439 " ideal model delta sigma weight residual 109.34 113.02 -3.68 2.08e+00 2.31e-01 3.13e+00 angle pdb=" CA ALA J 201 " pdb=" C ALA J 201 " pdb=" N SER J 202 " ideal model delta sigma weight residual 116.84 119.75 -2.91 1.71e+00 3.42e-01 2.89e+00 angle pdb=" N ALA J 201 " pdb=" CA ALA J 201 " pdb=" C ALA J 201 " ideal model delta sigma weight residual 110.80 114.32 -3.52 2.13e+00 2.20e-01 2.73e+00 angle pdb=" N GLU J 240 " pdb=" CA GLU J 240 " pdb=" C GLU J 240 " ideal model delta sigma weight residual 110.80 107.34 3.46 2.13e+00 2.20e-01 2.63e+00 ... (remaining 14140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 3333 11.94 - 23.88: 124 23.88 - 35.82: 35 35.82 - 47.76: 22 47.76 - 59.70: 22 Dihedral angle restraints: 3536 sinusoidal: 2036 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LEU J 258 " pdb=" CB LEU J 258 " pdb=" CG LEU J 258 " pdb=" CD1 LEU J 258 " ideal model delta sinusoidal sigma weight residual 180.00 139.07 40.93 3 1.50e+01 4.44e-03 7.31e+00 dihedral pdb=" CA LEU J 135 " pdb=" CB LEU J 135 " pdb=" CG LEU J 135 " pdb=" CD1 LEU J 135 " ideal model delta sinusoidal sigma weight residual 180.00 144.83 35.17 3 1.50e+01 4.44e-03 6.01e+00 dihedral pdb=" CA LYS J 347 " pdb=" CB LYS J 347 " pdb=" CG LYS J 347 " pdb=" CD LYS J 347 " ideal model delta sinusoidal sigma weight residual 60.00 90.68 -30.68 3 1.50e+01 4.44e-03 4.91e+00 ... (remaining 3533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 405 0.024 - 0.048: 126 0.048 - 0.072: 51 0.072 - 0.096: 22 0.096 - 0.120: 26 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 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA VAL J 188 " pdb=" N VAL J 188 " pdb=" C VAL J 188 " pdb=" CB VAL J 188 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE J 195 " pdb=" N ILE J 195 " pdb=" C ILE J 195 " pdb=" CB ILE J 195 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 627 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 254 " -0.006 5.00e-02 4.00e+02 9.72e-03 1.51e-01 pdb=" N PRO J 255 " 0.017 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " -0.005 5.00e-02 4.00e+02 pdb=" CD PRO J 255 " -0.005 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 9.06e-03 1.31e-01 pdb=" N PRO J 224 " -0.016 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 delta sigma weight rms_deltas residual plane pdb=" C GLY J 40 " 0.005 5.00e-02 4.00e+02 8.20e-03 1.08e-01 pdb=" N PRO J 41 " -0.014 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.004 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.005 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 543 2.24 - 2.83: 17924 2.83 - 3.42: 17879 3.42 - 4.01: 23299 4.01 - 4.60: 36615 Nonbonded interactions: 96260 Sorted by model distance: nonbonded pdb=" OD2 ASP J 451 " pdb=" H GLU J 454 " model vdw 1.646 1.850 nonbonded pdb=" OE1 GLU J 168 " pdb=" H GLU J 168 " model vdw 1.652 1.850 nonbonded pdb=" O LEU J 317 " pdb=" HG1 THR J 321 " model vdw 1.713 1.850 nonbonded pdb=" OE1 GLU J 245 " pdb=" H GLU J 245 " model vdw 1.720 1.850 nonbonded pdb=" OE1 GLU J 33 " pdb=" HE ARG J 36 " model vdw 1.728 1.850 ... (remaining 96255 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: 1.210 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: 0.120 Extract box with map and model: 4.630 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.230 Find NCS groups from input model: 0.130 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 0.021 3809 Z= 0.103 Angle : 0.353 5.628 5126 Z= 0.201 Chirality : 0.037 0.120 630 Planarity : 0.001 0.010 663 Dihedral : 4.651 40.926 1463 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.34 % Favored : 89.07 % 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: -4.05 (0.32), residues: 503 helix: -3.25 (0.22), residues: 193 sheet: -4.43 (0.45), residues: 62 loop : -1.55 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 296 PHE 0.002 0.000 PHE J 261 TYR 0.001 0.000 TYR J 297 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 51 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.4094 time to fit residues: 25.4974 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3809 Z= 0.156 Angle : 0.470 4.513 5126 Z= 0.259 Chirality : 0.039 0.131 630 Planarity : 0.002 0.013 663 Dihedral : 2.565 15.837 529 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % 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: -3.06 (0.33), residues: 503 helix: -1.32 (0.30), residues: 226 sheet: -3.55 (0.51), residues: 68 loop : -2.12 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 375 PHE 0.005 0.001 PHE J 261 TYR 0.007 0.001 TYR J 124 ARG 0.003 0.000 ARG J 425 *********************** 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 33 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.615 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: 33 average time/residue: 0.3782 time to fit residues: 15.8514 Evaluate side-chains 23 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 3.9990 chunk 14 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3809 Z= 0.156 Angle : 0.421 4.332 5126 Z= 0.232 Chirality : 0.037 0.118 630 Planarity : 0.002 0.015 663 Dihedral : 2.604 12.595 529 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -1.87 (0.36), residues: 503 helix: -0.23 (0.34), residues: 238 sheet: -3.02 (0.64), residues: 58 loop : -1.79 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 72 PHE 0.006 0.001 PHE J 261 TYR 0.003 0.001 TYR J 418 ARG 0.003 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 24 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2894 time to fit residues: 9.5230 Evaluate side-chains 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3809 Z= 0.261 Angle : 0.492 4.138 5126 Z= 0.277 Chirality : 0.037 0.116 630 Planarity : 0.003 0.017 663 Dihedral : 3.083 14.986 529 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -1.30 (0.38), residues: 503 helix: 0.23 (0.34), residues: 238 sheet: -2.73 (0.66), residues: 58 loop : -1.51 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 375 PHE 0.008 0.001 PHE J 261 TYR 0.003 0.001 TYR J 124 ARG 0.002 0.000 ARG J 346 *********************** 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 22 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.633 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: 0.2861 time to fit residues: 8.7204 Evaluate side-chains 18 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4795 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= 0.124 Angle : 0.372 4.013 5126 Z= 0.204 Chirality : 0.037 0.122 630 Planarity : 0.002 0.016 663 Dihedral : 2.766 12.584 529 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: -0.72 (0.38), residues: 503 helix: 0.68 (0.35), residues: 239 sheet: -2.53 (0.70), residues: 52 loop : -1.21 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.007 0.001 PHE J 261 TYR 0.004 0.001 TYR J 297 ARG 0.001 0.000 ARG J 493 *********************** 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 : 0.624 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: 22 average time/residue: 0.3053 time to fit residues: 9.5455 Evaluate side-chains 19 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3809 Z= 0.193 Angle : 0.422 4.146 5126 Z= 0.237 Chirality : 0.037 0.123 630 Planarity : 0.002 0.015 663 Dihedral : 3.042 13.559 529 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.39), residues: 503 helix: 0.70 (0.34), residues: 241 sheet: -2.29 (0.73), residues: 52 loop : -1.15 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 375 PHE 0.006 0.001 PHE J 261 TYR 0.004 0.001 TYR J 297 ARG 0.002 0.000 ARG J 346 *********************** 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 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.616 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: 0.3022 time to fit residues: 8.4046 Evaluate side-chains 18 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3809 Z= 0.315 Angle : 0.539 4.567 5126 Z= 0.306 Chirality : 0.038 0.145 630 Planarity : 0.003 0.030 663 Dihedral : 3.702 14.993 529 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % 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: -1.17 (0.36), residues: 503 helix: 0.06 (0.32), residues: 243 sheet: -2.42 (0.69), residues: 52 loop : -1.22 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.010 0.002 PHE J 285 TYR 0.005 0.001 TYR J 297 ARG 0.005 0.001 ARG J 370 *********************** 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 20 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.659 Fit side-chains 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: 0.3181 time to fit residues: 8.9424 Evaluate side-chains 18 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.6037 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= 0.164 Angle : 0.411 4.571 5126 Z= 0.228 Chirality : 0.037 0.120 630 Planarity : 0.002 0.028 663 Dihedral : 3.353 13.958 529 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % 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: -0.77 (0.37), residues: 503 helix: 0.52 (0.33), residues: 241 sheet: -2.30 (0.70), residues: 52 loop : -1.16 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 463 PHE 0.005 0.001 PHE J 261 TYR 0.005 0.001 TYR J 297 ARG 0.004 0.000 ARG J 370 *********************** 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 : 0.620 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: 0.3003 time to fit residues: 8.3868 Evaluate side-chains 18 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6054 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= 0.119 Angle : 0.383 5.517 5126 Z= 0.207 Chirality : 0.037 0.122 630 Planarity : 0.002 0.028 663 Dihedral : 3.075 12.634 529 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -0.23 (0.38), residues: 503 helix: 1.06 (0.34), residues: 240 sheet: -2.09 (0.73), residues: 52 loop : -0.99 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.006 0.001 PHE J 261 TYR 0.004 0.001 TYR J 297 ARG 0.003 0.000 ARG J 370 *********************** 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 : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 285 PHE cc_start: 0.8806 (m-80) cc_final: 0.8592 (m-80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2813 time to fit residues: 8.5270 Evaluate side-chains 19 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.6160 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= 0.142 Angle : 0.395 6.144 5126 Z= 0.216 Chirality : 0.037 0.122 630 Planarity : 0.002 0.030 663 Dihedral : 3.076 12.755 529 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -0.18 (0.39), residues: 503 helix: 1.13 (0.34), residues: 241 sheet: -1.81 (0.71), residues: 58 loop : -1.07 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.005 0.001 PHE J 261 TYR 0.003 0.001 TYR J 297 ARG 0.003 0.000 ARG J 370 ********************** 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 22 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 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 outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2954 time to fit residues: 9.0214 Evaluate side-chains 18 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 0.0870 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.054220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.036589 restraints weight = 78030.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037944 restraints weight = 37529.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.038816 restraints weight = 22759.824| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.6177 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= 0.112 Angle : 0.375 6.199 5126 Z= 0.202 Chirality : 0.037 0.125 630 Planarity : 0.002 0.027 663 Dihedral : 2.938 12.301 529 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 0.09 (0.39), residues: 503 helix: 1.37 (0.35), residues: 240 sheet: -1.44 (0.69), residues: 70 loop : -0.96 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.006 0.001 PHE J 261 TYR 0.002 0.000 TYR J 297 ARG 0.003 0.000 ARG J 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.40 seconds wall clock time: 43 minutes 3.57 seconds (2583.57 seconds total)