Starting phenix.real_space_refine on Thu Jan 18 03:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9e_24324/01_2024/7r9e_24324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9e_24324/01_2024/7r9e_24324.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/7r9e_24324/01_2024/7r9e_24324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9e_24324/01_2024/7r9e_24324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9e_24324/01_2024/7r9e_24324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9e_24324/01_2024/7r9e_24324.pdb" } 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 3938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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-1.21-5211/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: 3.91, per 1000 atoms: 0.51 Number of scatterers: 7726 At special positions: 0 Unit cell: (91.8, 66.96, 111.24, 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: 5.56 Conformation dependent library (CDL) restraints added in 770.5 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: 18 helices and 4 sheets defined 52.5% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'J' and resid 20 through 37 removed outlier: 3.605A pdb=" N THR J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL J 35 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 67 removed outlier: 3.968A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 89 removed outlier: 4.134A pdb=" N LEU J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL J 81 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN J 85 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU J 88 " --> pdb=" O THR J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 112 removed outlier: 3.852A pdb=" N ALA J 96 " --> pdb=" O GLY J 92 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU J 102 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU J 109 " --> pdb=" O ARG J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 139 removed outlier: 3.534A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY J 123 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR J 124 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN J 129 " --> pdb=" O GLN J 125 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 162 removed outlier: 4.120A pdb=" N LYS J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER J 157 " --> pdb=" O ILE J 153 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR J 159 " --> pdb=" O MET J 155 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 179 removed outlier: 3.568A pdb=" N GLU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE J 174 " --> pdb=" O LEU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'J' and resid 260 through 280 removed outlier: 3.975A pdb=" N GLU J 266 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET J 268 " --> pdb=" O GLN J 264 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU J 269 " --> pdb=" O GLU J 265 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS J 270 " --> pdb=" O GLU J 266 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP J 271 " --> pdb=" O LYS J 267 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET J 272 " --> pdb=" O MET J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 302 removed outlier: 3.652A pdb=" N GLN J 295 " --> pdb=" O ASP J 291 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA J 299 " --> pdb=" O GLN J 295 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS J 300 " --> pdb=" O HIS J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.770A pdb=" N GLU J 315 " --> pdb=" O LYS J 311 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS J 316 " --> pdb=" O SER J 312 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 317 " --> pdb=" O ASP J 313 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA J 318 " --> pdb=" O MET J 314 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS J 319 " --> pdb=" O GLU J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 397 removed outlier: 3.500A pdb=" N ILE J 377 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP J 386 " --> pdb=" O ARG J 382 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL J 388 " --> pdb=" O VAL J 384 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS J 393 " --> pdb=" O GLY J 389 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR J 394 " --> pdb=" O VAL J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 420 removed outlier: 3.720A pdb=" N LEU J 411 " --> pdb=" O THR J 407 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS J 414 " --> pdb=" O GLU J 410 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG J 416 " --> pdb=" O SER J 412 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU J 417 " --> pdb=" O MET J 413 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 420 " --> pdb=" O ARG J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 437 removed outlier: 3.620A pdb=" N VAL J 430 " --> pdb=" O GLU J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 449 removed outlier: 3.729A pdb=" N ARG J 442 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU J 444 " --> pdb=" O ILE J 440 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 463 removed outlier: 4.471A pdb=" N VAL J 457 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA J 461 " --> pdb=" O VAL J 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS J 463 " --> pdb=" O VAL J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 487 Processing helix chain 'J' and resid 492 through 511 removed outlier: 3.552A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) removed outlier: 4.287A 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: 3.666A pdb=" N VAL J 401 " --> pdb=" O GLU J 490 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU J 490 " --> pdb=" O VAL J 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.543A pdb=" N MET J 367 " --> pdb=" O LYS J 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 284 through 285 removed outlier: 5.648A pdb=" N LEU J 284 " --> pdb=" O ALA J 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 471 through 473 121 hydrogen bonds defined for protein. 360 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: 2.23 Time building geometry restraints manager: 5.79 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 HIS J 361 " pdb=" N PRO J 362 " ideal model delta sigma weight residual 1.326 1.337 -0.010 1.44e-02 4.82e+03 5.23e-01 bond pdb=" N ILE J 455 " pdb=" CA ILE J 455 " ideal model delta sigma weight residual 1.452 1.460 -0.008 1.18e-02 7.18e+03 4.09e-01 bond pdb=" C GLU J 490 " pdb=" N PRO J 491 " ideal model delta sigma weight residual 1.331 1.338 -0.007 1.21e-02 6.83e+03 3.54e-01 bond pdb=" CA ALA J 364 " pdb=" C ALA J 364 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.34e-02 5.57e+03 3.09e-01 bond pdb=" N HIS J 361 " pdb=" CA HIS J 361 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.41e-02 5.03e+03 2.63e-01 ... (remaining 7742 not shown) Histogram of bond angle deviations from ideal: 100.87 - 106.94: 57 106.94 - 113.02: 9886 113.02 - 119.10: 1574 119.10 - 125.17: 2577 125.17 - 131.25: 51 Bond angle restraints: 14145 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 112.96 109.50 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" N ILE J 440 " pdb=" CA ILE J 440 " pdb=" C ILE J 440 " ideal model delta sigma weight residual 112.35 109.25 3.10 1.20e+00 6.94e-01 6.68e+00 angle pdb=" N ASN J 236 " pdb=" CA ASN J 236 " pdb=" C ASN J 236 " ideal model delta sigma weight residual 114.62 112.10 2.52 1.14e+00 7.69e-01 4.88e+00 angle pdb=" C VAL J 439 " pdb=" N ILE J 440 " pdb=" CA ILE J 440 " ideal model delta sigma weight residual 120.33 122.04 -1.71 8.00e-01 1.56e+00 4.54e+00 angle pdb=" CA ASN J 236 " pdb=" C ASN J 236 " pdb=" N CYS J 237 " ideal model delta sigma weight residual 119.71 117.38 2.33 1.17e+00 7.31e-01 3.98e+00 ... (remaining 14140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3409 17.35 - 34.71: 43 34.71 - 52.06: 9 52.06 - 69.42: 1 69.42 - 86.77: 2 Dihedral angle restraints: 3464 sinusoidal: 1964 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LYS J 300 " pdb=" CB LYS J 300 " pdb=" CG LYS J 300 " pdb=" CD LYS J 300 " ideal model delta sinusoidal sigma weight residual -60.00 -97.60 37.60 3 1.50e+01 4.44e-03 6.58e+00 dihedral pdb=" CA ARG J 18 " pdb=" CB ARG J 18 " pdb=" CG ARG J 18 " pdb=" CD ARG J 18 " ideal model delta sinusoidal sigma weight residual -60.00 -95.59 35.59 3 1.50e+01 4.44e-03 6.11e+00 dihedral pdb=" CA VAL J 304 " pdb=" CB VAL J 304 " pdb=" CG2 VAL J 304 " pdb="HG23 VAL J 304 " ideal model delta sinusoidal sigma weight residual 240.00 153.23 86.77 2 3.00e+01 1.11e-03 5.32e+00 ... (remaining 3461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 374 0.024 - 0.047: 155 0.047 - 0.071: 48 0.071 - 0.095: 25 0.095 - 0.118: 28 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA VAL J 227 " pdb=" N VAL J 227 " pdb=" C VAL J 227 " pdb=" CB VAL J 227 " 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 369 " pdb=" N ILE J 369 " pdb=" C ILE J 369 " pdb=" CB ILE J 369 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-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 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 627 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS J 361 " 0.010 5.00e-02 4.00e+02 1.51e-02 3.66e-01 pdb=" N PRO J 362 " -0.026 5.00e-02 4.00e+02 pdb=" CA PRO J 362 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO J 362 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS J 116 " 0.009 5.00e-02 4.00e+02 1.33e-02 2.82e-01 pdb=" N PRO J 117 " -0.023 5.00e-02 4.00e+02 pdb=" CA PRO J 117 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO J 117 " 0.007 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 254 " -0.008 5.00e-02 4.00e+02 1.28e-02 2.62e-01 pdb=" N PRO J 255 " 0.022 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " -0.007 5.00e-02 4.00e+02 pdb=" CD PRO J 255 " -0.007 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 1093 2.28 - 2.86: 18245 2.86 - 3.44: 17610 3.44 - 4.02: 22505 4.02 - 4.60: 35020 Nonbonded interactions: 94473 Sorted by model distance: nonbonded pdb=" O ASP J 482 " pdb="HD21 ASN J 486 " model vdw 1.705 1.850 nonbonded pdb=" OE1 GLU J 240 " pdb=" H GLU J 240 " model vdw 1.710 1.850 nonbonded pdb=" O CYS J 470 " pdb=" H MET J 483 " model vdw 1.736 1.850 nonbonded pdb=" O VAL J 409 " pdb=" HG SER J 412 " model vdw 1.742 1.850 nonbonded pdb=" O SER J 199 " pdb=" HE ARG J 370 " model vdw 1.745 1.850 ... (remaining 94468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 4.680 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.640 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.013 3809 Z= 0.100 Angle : 0.375 4.097 5126 Z= 0.235 Chirality : 0.037 0.118 630 Planarity : 0.001 0.015 663 Dihedral : 4.449 37.604 1463 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 1.39 % Allowed : 9.94 % Favored : 88.67 % 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: -3.58 (0.34), residues: 503 helix: -3.22 (0.26), residues: 179 sheet: -3.44 (0.83), residues: 33 loop : -1.64 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 296 PHE 0.003 0.001 PHE J 285 TYR 0.001 0.000 TYR J 418 ARG 0.002 0.000 ARG J 346 *********************** 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 47 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 367 MET cc_start: 0.8076 (mmm) cc_final: 0.7826 (tpp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3293 time to fit residues: 19.5666 Evaluate side-chains 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 0.0060 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 72 HIS J 236 ASN J 500 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3809 Z= 0.178 Angle : 0.541 5.052 5126 Z= 0.300 Chirality : 0.040 0.123 630 Planarity : 0.003 0.030 663 Dihedral : 2.878 19.802 529 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.57 % Favored : 94.23 % Rotamer: Outliers : 0.98 % Allowed : 5.90 % Favored : 93.12 % 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: -3.12 (0.33), residues: 503 helix: -1.69 (0.31), residues: 215 sheet: -2.68 (1.04), residues: 26 loop : -2.34 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.008 0.002 PHE J 355 TYR 0.004 0.001 TYR J 418 ARG 0.002 0.000 ARG J 29 *********************** 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 31 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 268 MET cc_start: 0.8392 (tmm) cc_final: 0.8079 (ppp) REVERT: J 367 MET cc_start: 0.8240 (mmm) cc_final: 0.7989 (tpp) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.3137 time to fit residues: 11.4107 Evaluate side-chains 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 77 MET Chi-restraints excluded: chain J residue 375 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.3217 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= 0.158 Angle : 0.461 5.020 5126 Z= 0.249 Chirality : 0.038 0.120 630 Planarity : 0.003 0.028 663 Dihedral : 2.968 15.099 529 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.23 % Allowed : 5.41 % 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: -2.20 (0.36), residues: 503 helix: -0.66 (0.34), residues: 239 sheet: -2.66 (0.99), residues: 26 loop : -2.14 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.012 0.001 PHE J 355 TYR 0.001 0.000 TYR J 124 ARG 0.002 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: 5 poor density : 23 time to evaluate : 0.643 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: 5 outliers final: 3 residues processed: 26 average time/residue: 0.3088 time to fit residues: 10.8554 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 72 HIS 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: 0.6980 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.0070 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 27 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.3660 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= 0.143 Angle : 0.443 6.048 5126 Z= 0.236 Chirality : 0.038 0.115 630 Planarity : 0.002 0.028 663 Dihedral : 2.959 14.808 529 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.23 % Allowed : 5.65 % Favored : 93.12 % 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: -1.69 (0.37), residues: 503 helix: -0.22 (0.34), residues: 243 sheet: -2.47 (0.99), residues: 26 loop : -1.94 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 116 PHE 0.005 0.001 PHE J 355 TYR 0.003 0.001 TYR J 297 ARG 0.001 0.000 ARG J 29 *********************** 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 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.3103 time to fit residues: 10.4823 Evaluate side-chains 26 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 367 MET 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: 10.0000 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8415 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3809 Z= 0.201 Angle : 0.482 5.153 5126 Z= 0.261 Chirality : 0.038 0.136 630 Planarity : 0.003 0.026 663 Dihedral : 3.014 14.305 529 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.47 % Allowed : 6.14 % Favored : 92.38 % 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: -1.23 (0.38), residues: 503 helix: 0.18 (0.34), residues: 239 sheet: -2.28 (0.92), residues: 26 loop : -1.67 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 116 PHE 0.006 0.001 PHE J 355 TYR 0.002 0.001 TYR J 418 ARG 0.002 0.000 ARG J 370 *********************** 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 30 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 27 average time/residue: 0.2981 time to fit residues: 10.9261 Evaluate side-chains 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 367 MET 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: 0.6980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.4464 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= 0.127 Angle : 0.425 5.183 5126 Z= 0.225 Chirality : 0.038 0.119 630 Planarity : 0.002 0.027 663 Dihedral : 2.949 13.662 529 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.23 % Allowed : 6.39 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.38), residues: 503 helix: 0.58 (0.34), residues: 240 sheet: -1.99 (0.94), residues: 26 loop : -1.49 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.005 0.001 PHE J 433 TYR 0.002 0.000 TYR J 297 ARG 0.001 0.000 ARG J 511 *********************** 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 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.3170 time to fit residues: 11.0797 Evaluate side-chains 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 72 HIS Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 367 MET 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: 8.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3809 Z= 0.276 Angle : 0.528 4.867 5126 Z= 0.296 Chirality : 0.038 0.117 630 Planarity : 0.003 0.027 663 Dihedral : 3.217 14.179 529 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.98 % Allowed : 6.88 % Favored : 92.14 % 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 (0.37), residues: 503 helix: 0.58 (0.33), residues: 239 sheet: -1.94 (0.93), residues: 26 loop : -1.58 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 116 PHE 0.006 0.001 PHE J 355 TYR 0.003 0.001 TYR J 418 ARG 0.003 0.000 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 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.3157 time to fit residues: 10.2609 Evaluate side-chains 23 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 72 HIS 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: 0.0000 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.0070 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4602 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.5039 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 : 0.442 5.510 5126 Z= 0.231 Chirality : 0.038 0.122 630 Planarity : 0.002 0.026 663 Dihedral : 3.055 12.278 529 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.23 % Allowed : 7.13 % Favored : 91.65 % 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: -0.48 (0.38), residues: 503 helix: 0.92 (0.34), residues: 239 sheet: -1.75 (0.95), residues: 26 loop : -1.46 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.006 0.001 PHE J 355 TYR 0.002 0.000 TYR J 297 ARG 0.002 0.000 ARG J 22 *********************** 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 25 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.3260 time to fit residues: 10.4824 Evaluate side-chains 23 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 87 LYS 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: 2.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.0070 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.8400 moved from start: 0.5175 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= 0.124 Angle : 0.449 6.350 5126 Z= 0.234 Chirality : 0.038 0.125 630 Planarity : 0.002 0.027 663 Dihedral : 2.995 11.762 529 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.49 % Allowed : 7.37 % Favored : 92.14 % 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: -0.32 (0.38), residues: 503 helix: 1.04 (0.34), residues: 240 sheet: -1.70 (0.95), residues: 26 loop : -1.37 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 116 PHE 0.005 0.001 PHE J 433 TYR 0.002 0.000 TYR J 297 ARG 0.002 0.000 ARG J 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.3340 time to fit residues: 10.3418 Evaluate side-chains 22 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 87 LYS 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: 10.0000 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 0.1980 chunk 42 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8395 moved from start: 0.5251 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= 0.122 Angle : 0.454 6.490 5126 Z= 0.236 Chirality : 0.038 0.120 630 Planarity : 0.002 0.027 663 Dihedral : 2.975 11.992 529 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.49 % Allowed : 6.88 % Favored : 92.63 % 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: -0.21 (0.39), residues: 503 helix: 1.11 (0.35), residues: 239 sheet: -1.64 (0.95), residues: 26 loop : -1.28 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.005 0.001 PHE J 433 TYR 0.002 0.000 TYR J 297 ARG 0.002 0.000 ARG J 346 ********************** 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: 2 poor density : 20 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.3354 time to fit residues: 9.8693 Evaluate side-chains 22 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 87 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.073611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046690 restraints weight = 74568.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048138 restraints weight = 34284.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.048899 restraints weight = 20736.282| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5427 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= 0.163 Angle : 0.467 6.285 5126 Z= 0.248 Chirality : 0.038 0.123 630 Planarity : 0.002 0.026 663 Dihedral : 3.003 12.103 529 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.74 % Allowed : 6.63 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.38), residues: 503 helix: 1.12 (0.35), residues: 239 sheet: -1.58 (0.96), residues: 26 loop : -1.26 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS J 116 PHE 0.004 0.001 PHE J 355 TYR 0.002 0.001 TYR J 124 ARG 0.002 0.000 ARG J 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.18 seconds wall clock time: 42 minutes 57.68 seconds (2577.68 seconds total)