Starting phenix.real_space_refine on Thu Feb 15 02:53:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x67_22072/02_2024/6x67_22072.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x67_22072/02_2024/6x67_22072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x67_22072/02_2024/6x67_22072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x67_22072/02_2024/6x67_22072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x67_22072/02_2024/6x67_22072.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x67_22072/02_2024/6x67_22072.pdb" } resolution = 3.47 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= 0.003 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 158 5.49 5 S 88 5.16 5 C 6413 2.51 5 N 1953 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10984 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "D" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "E" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 762 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "F" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 961 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "G" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "K" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 717 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "L" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3568 SG CYS C 559 44.667 25.532 50.448 1.00 96.71 S ATOM 3593 SG CYS C 562 44.522 22.338 51.255 1.00 99.50 S ATOM 3747 SG CYS C 582 44.160 23.439 47.991 1.00107.27 S ATOM 3684 SG CYS C 574 38.869 35.104 47.373 1.00152.47 S ATOM 3708 SG CYS C 577 39.538 35.442 50.590 1.00153.59 S ATOM 3815 SG CYS C 590 37.374 32.630 49.357 1.00160.83 S ATOM 3836 SG CYS C 593 36.317 35.624 49.163 1.00169.71 S ATOM 7416 SG CYS D 559 37.258 28.178 26.376 1.00261.70 S ATOM 7441 SG CYS D 562 39.984 28.518 24.406 1.00266.25 S ATOM 7595 SG CYS D 582 40.202 28.443 28.046 1.00241.26 S ATOM 7532 SG CYS D 574 30.661 29.621 35.861 1.00239.63 S ATOM 7556 SG CYS D 577 28.278 29.558 33.616 1.00244.66 S ATOM 7663 SG CYS D 590 30.865 32.084 33.669 1.00249.59 S ATOM 7684 SG CYS D 593 28.715 31.926 35.920 1.00249.56 S Time building chain proxies: 5.43, per 1000 atoms: 0.49 Number of scatterers: 10984 At special positions: 0 Unit cell: (91.16, 89.04, 148.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 88 16.00 P 158 15.00 O 2364 8.00 N 1953 7.00 C 6413 6.00 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: 7.07 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 582 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 559 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 585 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 590 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 574 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 593 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 577 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 562 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 585 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 582 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 559 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 574 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 590 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 593 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 577 " Number of angles added : 18 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 42.6% alpha, 11.3% beta 69 base pairs and 122 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 132 through 156 removed outlier: 4.457A pdb=" N PHE C 138 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLU C 142 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 189 Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.650A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.589A pdb=" N LEU C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 258 removed outlier: 4.543A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 446 through 456 Processing helix chain 'C' and resid 464 through 493 removed outlier: 3.966A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 469 " --> pdb=" O TRP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 519 removed outlier: 5.088A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.695A pdb=" N ARG D 126 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 139 through 156 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 172 through 190 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.379A pdb=" N LYS D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 334 through 337 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 433 through 443 Processing helix chain 'D' and resid 446 through 456 Processing helix chain 'D' and resid 464 through 493 removed outlier: 3.866A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 519 removed outlier: 5.091A pdb=" N SER D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 534 Processing sheet with id=AA1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.998A pdb=" N MET C 306 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP C 300 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 265 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 370 " --> pdb=" O CYS C 345 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR C 415 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 572 through 573 Processing sheet with id=AA4, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.553A pdb=" N ASP D 300 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET D 306 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.348A pdb=" N LEU D 265 " --> pdb=" O THR D 344 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 370 " --> pdb=" O CYS D 345 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR D 415 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 572 through 573 322 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 171 hydrogen bonds 342 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 122 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2427 1.33 - 1.45: 3635 1.45 - 1.58: 5026 1.58 - 1.70: 304 1.70 - 1.83: 136 Bond restraints: 11528 Sorted by residual: bond pdb=" C PRO C 288 " pdb=" N SER C 289 " ideal model delta sigma weight residual 1.331 1.239 0.093 1.38e-02 5.25e+03 4.51e+01 bond pdb=" O3' DT J 21 " pdb=" P DA J 22 " ideal model delta sigma weight residual 1.607 1.515 0.092 1.50e-02 4.44e+03 3.79e+01 bond pdb=" O3' DT K -23 " pdb=" P DT K -22 " ideal model delta sigma weight residual 1.607 1.691 -0.084 1.50e-02 4.44e+03 3.15e+01 bond pdb=" N SER D 289 " pdb=" CA SER D 289 " ideal model delta sigma weight residual 1.459 1.391 0.067 1.22e-02 6.72e+03 3.05e+01 bond pdb=" N TRP D 248 " pdb=" CA TRP D 248 " ideal model delta sigma weight residual 1.459 1.394 0.065 1.19e-02 7.06e+03 2.98e+01 ... (remaining 11523 not shown) Histogram of bond angle deviations from ideal: 91.26 - 101.97: 239 101.97 - 112.68: 6675 112.68 - 123.39: 7981 123.39 - 134.09: 1341 134.09 - 144.80: 2 Bond angle restraints: 16238 Sorted by residual: angle pdb=" C3' DT K -23 " pdb=" O3' DT K -23 " pdb=" P DT K -22 " ideal model delta sigma weight residual 120.20 144.80 -24.60 1.50e+00 4.44e-01 2.69e+02 angle pdb=" C3' DT J 21 " pdb=" O3' DT J 21 " pdb=" P DA J 22 " ideal model delta sigma weight residual 120.20 101.85 18.35 1.50e+00 4.44e-01 1.50e+02 angle pdb=" O3' DT K -23 " pdb=" P DT K -22 " pdb=" O5' DT K -22 " ideal model delta sigma weight residual 104.00 118.83 -14.83 1.50e+00 4.44e-01 9.78e+01 angle pdb=" CA HIS D 193 " pdb=" CB HIS D 193 " pdb=" CG HIS D 193 " ideal model delta sigma weight residual 113.80 104.11 9.69 1.00e+00 1.00e+00 9.39e+01 angle pdb=" N ARG D 556 " pdb=" CA ARG D 556 " pdb=" C ARG D 556 " ideal model delta sigma weight residual 110.80 91.26 19.54 2.13e+00 2.20e-01 8.41e+01 ... (remaining 16233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 5411 22.74 - 45.48: 878 45.48 - 68.23: 328 68.23 - 90.97: 12 90.97 - 113.71: 1 Dihedral angle restraints: 6630 sinusoidal: 3814 harmonic: 2816 Sorted by residual: dihedral pdb=" C PRO D 362 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " pdb=" CB PRO D 362 " ideal model delta harmonic sigma weight residual -120.70 -105.48 -15.22 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" C PRO D 285 " pdb=" N PRO D 285 " pdb=" CA PRO D 285 " pdb=" CB PRO D 285 " ideal model delta harmonic sigma weight residual -120.70 -106.96 -13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C PRO C 541 " pdb=" N PRO C 541 " pdb=" CA PRO C 541 " pdb=" CB PRO C 541 " ideal model delta harmonic sigma weight residual -120.70 -108.54 -12.16 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1487 0.120 - 0.239: 265 0.239 - 0.359: 42 0.359 - 0.478: 5 0.478 - 0.598: 1 Chirality restraints: 1800 Sorted by residual: chirality pdb=" P DT K -22 " pdb=" OP1 DT K -22 " pdb=" OP2 DT K -22 " pdb=" O5' DT K -22 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CA PRO D 233 " pdb=" N PRO D 233 " pdb=" C PRO D 233 " pdb=" CB PRO D 233 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA PRO C 537 " pdb=" N PRO C 537 " pdb=" C PRO C 537 " pdb=" CB PRO C 537 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1797 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA E 25 " 0.141 2.00e-02 2.50e+03 6.23e-02 1.07e+02 pdb=" N9 DA E 25 " -0.009 2.00e-02 2.50e+03 pdb=" C8 DA E 25 " -0.064 2.00e-02 2.50e+03 pdb=" N7 DA E 25 " -0.060 2.00e-02 2.50e+03 pdb=" C5 DA E 25 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DA E 25 " 0.024 2.00e-02 2.50e+03 pdb=" N6 DA E 25 " 0.094 2.00e-02 2.50e+03 pdb=" N1 DA E 25 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DA E 25 " -0.040 2.00e-02 2.50e+03 pdb=" N3 DA E 25 " -0.057 2.00e-02 2.50e+03 pdb=" C4 DA E 25 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 21 " 0.081 2.00e-02 2.50e+03 3.69e-02 3.40e+01 pdb=" N1 DT J 21 " -0.016 2.00e-02 2.50e+03 pdb=" C2 DT J 21 " -0.014 2.00e-02 2.50e+03 pdb=" O2 DT J 21 " -0.042 2.00e-02 2.50e+03 pdb=" N3 DT J 21 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DT J 21 " 0.014 2.00e-02 2.50e+03 pdb=" O4 DT J 21 " 0.038 2.00e-02 2.50e+03 pdb=" C5 DT J 21 " -0.022 2.00e-02 2.50e+03 pdb=" C7 DT J 21 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT J 21 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K -23 " 0.041 2.00e-02 2.50e+03 3.26e-02 2.66e+01 pdb=" N1 DT K -23 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT K -23 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT K -23 " -0.066 2.00e-02 2.50e+03 pdb=" N3 DT K -23 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DT K -23 " 0.014 2.00e-02 2.50e+03 pdb=" O4 DT K -23 " 0.038 2.00e-02 2.50e+03 pdb=" C5 DT K -23 " -0.011 2.00e-02 2.50e+03 pdb=" C7 DT K -23 " -0.045 2.00e-02 2.50e+03 pdb=" C6 DT K -23 " -0.003 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 216 2.60 - 3.18: 9164 3.18 - 3.75: 17872 3.75 - 4.33: 26051 4.33 - 4.90: 38247 Nonbonded interactions: 91550 Sorted by model distance: nonbonded pdb=" OD2 ASP C 346 " pdb="CA CA C 603 " model vdw 2.028 2.510 nonbonded pdb=" OD2 ASP D 346 " pdb="CA CA D 603 " model vdw 2.034 2.510 nonbonded pdb=" OP1 DT K 0 " pdb="CA CA C 603 " model vdw 2.067 2.510 nonbonded pdb=" OP1 DT F 0 " pdb="CA CA D 603 " model vdw 2.074 2.510 nonbonded pdb=" OD2 ASP C 218 " pdb="CA CA C 604 " model vdw 2.126 2.510 ... (remaining 91545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'L' } 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 individual isotropic 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: 0.570 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: 0.010 Extract box with map and model: 2.110 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 35.190 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.015 0.135 11528 Z= 0.886 Angle : 1.840 24.603 16238 Z= 1.224 Chirality : 0.096 0.598 1800 Planarity : 0.005 0.062 1508 Dihedral : 21.586 113.710 4810 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.84 % Allowed : 4.62 % Favored : 94.54 % Rotamer: Outliers : 0.23 % Allowed : 7.47 % Favored : 92.31 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.26), residues: 952 helix: -0.85 (0.23), residues: 377 sheet: 0.72 (0.50), residues: 116 loop : -0.44 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.011 TRP D 150 HIS 0.010 0.003 HIS D 487 PHE 0.022 0.006 PHE C 502 TYR 0.038 0.008 TYR D 406 ARG 0.006 0.001 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.8909 (tpp) cc_final: 0.8663 (tpp) REVERT: C 326 GLU cc_start: 0.6220 (mp0) cc_final: 0.5899 (mp0) REVERT: C 418 SER cc_start: 0.8017 (t) cc_final: 0.6897 (p) REVERT: C 503 MET cc_start: 0.9163 (mmm) cc_final: 0.8896 (mmm) REVERT: C 535 ILE cc_start: 0.8721 (mt) cc_final: 0.8511 (mt) REVERT: D 175 GLU cc_start: 0.7988 (tt0) cc_final: 0.7740 (tt0) REVERT: D 189 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7923 (mtp85) REVERT: D 255 CYS cc_start: 0.8310 (m) cc_final: 0.7934 (m) REVERT: D 259 TYR cc_start: 0.8072 (t80) cc_final: 0.7849 (t80) REVERT: D 305 TYR cc_start: 0.8723 (t80) cc_final: 0.8192 (t80) REVERT: D 418 SER cc_start: 0.8455 (t) cc_final: 0.8147 (p) REVERT: D 447 ASP cc_start: 0.8274 (p0) cc_final: 0.7984 (p0) REVERT: D 458 CYS cc_start: 0.8919 (t) cc_final: 0.8664 (p) outliers start: 2 outliers final: 0 residues processed: 417 average time/residue: 0.2705 time to fit residues: 149.5891 Evaluate side-chains 269 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS C 440 ASN C 475 ASN C 487 HIS ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS D 505 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11528 Z= 0.264 Angle : 0.755 8.467 16238 Z= 0.419 Chirality : 0.042 0.162 1800 Planarity : 0.004 0.031 1508 Dihedral : 24.210 121.050 2824 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.99 % Favored : 95.59 % Rotamer: Outliers : 3.39 % Allowed : 20.48 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.27), residues: 952 helix: 0.68 (0.27), residues: 377 sheet: 0.74 (0.48), residues: 109 loop : -0.67 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 150 HIS 0.008 0.002 HIS D 487 PHE 0.015 0.002 PHE C 482 TYR 0.022 0.002 TYR C 283 ARG 0.010 0.001 ARG D 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 0.995 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: C 238 ASN cc_start: 0.7814 (m-40) cc_final: 0.7353 (t0) REVERT: C 376 ARG cc_start: 0.8391 (tmt170) cc_final: 0.7868 (ttt-90) REVERT: C 394 MET cc_start: 0.8228 (mtp) cc_final: 0.7813 (ttm) REVERT: C 555 LYS cc_start: 0.9147 (mmtm) cc_final: 0.8885 (mptt) REVERT: C 586 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: D 154 GLU cc_start: 0.8315 (tp30) cc_final: 0.8070 (tp30) REVERT: D 305 TYR cc_start: 0.8861 (t80) cc_final: 0.8391 (t80) REVERT: D 342 ASN cc_start: 0.8772 (t0) cc_final: 0.8519 (t0) REVERT: D 438 TYR cc_start: 0.8706 (t80) cc_final: 0.8277 (t80) REVERT: D 447 ASP cc_start: 0.8031 (p0) cc_final: 0.7413 (p0) REVERT: D 452 MET cc_start: 0.8591 (mtp) cc_final: 0.8358 (mtp) outliers start: 30 outliers final: 14 residues processed: 329 average time/residue: 0.1936 time to fit residues: 89.7774 Evaluate side-chains 264 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 586 ASN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 475 ASN C 487 HIS ** C 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 GLN D 487 HIS D 531 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11528 Z= 0.228 Angle : 0.684 6.847 16238 Z= 0.376 Chirality : 0.039 0.150 1800 Planarity : 0.004 0.045 1508 Dihedral : 24.165 130.844 2824 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 3.62 % Allowed : 22.40 % Favored : 73.98 % 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: 0.20 (0.27), residues: 952 helix: 1.24 (0.27), residues: 371 sheet: 0.76 (0.46), residues: 108 loop : -0.93 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 465 HIS 0.006 0.001 HIS D 487 PHE 0.017 0.001 PHE C 251 TYR 0.017 0.001 TYR C 283 ARG 0.007 0.001 ARG D 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8646 (tt) REVERT: C 206 MET cc_start: 0.8499 (tpp) cc_final: 0.8212 (mmt) REVERT: C 238 ASN cc_start: 0.7869 (m-40) cc_final: 0.7310 (t0) REVERT: C 376 ARG cc_start: 0.8269 (tmt170) cc_final: 0.7990 (ttt-90) REVERT: C 394 MET cc_start: 0.8241 (mtp) cc_final: 0.7945 (ttm) REVERT: D 154 GLU cc_start: 0.8256 (tp30) cc_final: 0.7980 (tp30) REVERT: D 269 GLU cc_start: 0.7725 (pp20) cc_final: 0.7338 (pp20) REVERT: D 332 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8785 (mm) REVERT: D 447 ASP cc_start: 0.7983 (p0) cc_final: 0.7467 (p0) REVERT: D 452 MET cc_start: 0.8556 (mtp) cc_final: 0.8322 (mtp) outliers start: 32 outliers final: 18 residues processed: 286 average time/residue: 0.2024 time to fit residues: 82.6851 Evaluate side-chains 266 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 246 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 469 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 441 GLN D 342 ASN D 434 GLN D 531 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11528 Z= 0.376 Angle : 0.730 7.999 16238 Z= 0.399 Chirality : 0.043 0.150 1800 Planarity : 0.005 0.048 1508 Dihedral : 24.252 125.123 2824 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 6.00 % Allowed : 20.70 % Favored : 73.30 % 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: 0.04 (0.27), residues: 952 helix: 1.27 (0.27), residues: 370 sheet: 0.41 (0.48), residues: 107 loop : -1.10 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 348 HIS 0.011 0.002 HIS C 585 PHE 0.015 0.002 PHE C 179 TYR 0.018 0.002 TYR C 283 ARG 0.007 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 256 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 198 ASP cc_start: 0.8654 (m-30) cc_final: 0.8437 (m-30) REVERT: C 238 ASN cc_start: 0.7985 (m-40) cc_final: 0.7390 (t0) REVERT: C 269 GLU cc_start: 0.8804 (pm20) cc_final: 0.8603 (pm20) REVERT: C 306 MET cc_start: 0.9052 (tpp) cc_final: 0.8731 (tpt) REVERT: C 376 ARG cc_start: 0.8315 (tmt170) cc_final: 0.8024 (ttt-90) REVERT: C 394 MET cc_start: 0.8293 (mtp) cc_final: 0.8058 (ttm) REVERT: C 406 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.5727 (p90) REVERT: C 434 GLN cc_start: 0.8670 (tp40) cc_final: 0.8446 (tp40) REVERT: D 154 GLU cc_start: 0.8301 (tp30) cc_final: 0.8046 (tp30) REVERT: D 332 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8854 (mm) REVERT: D 372 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8807 (ttm110) REVERT: D 418 SER cc_start: 0.9049 (t) cc_final: 0.8770 (p) REVERT: D 447 ASP cc_start: 0.8070 (p0) cc_final: 0.7596 (p0) REVERT: D 452 MET cc_start: 0.8585 (mtp) cc_final: 0.8323 (mtp) REVERT: D 458 CYS cc_start: 0.8964 (t) cc_final: 0.8595 (p) outliers start: 53 outliers final: 36 residues processed: 283 average time/residue: 0.1827 time to fit residues: 74.6493 Evaluate side-chains 273 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 426 ILE Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 532 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 497 GLN C 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11528 Z= 0.197 Angle : 0.659 6.103 16238 Z= 0.361 Chirality : 0.038 0.147 1800 Planarity : 0.004 0.057 1508 Dihedral : 23.933 122.190 2824 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 2.94 % Allowed : 24.43 % Favored : 72.62 % 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: 0.13 (0.28), residues: 952 helix: 1.50 (0.28), residues: 377 sheet: 0.59 (0.47), residues: 104 loop : -1.26 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 465 HIS 0.004 0.001 HIS C 585 PHE 0.010 0.001 PHE C 482 TYR 0.015 0.001 TYR D 305 ARG 0.008 0.000 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: C 238 ASN cc_start: 0.7906 (m-40) cc_final: 0.7413 (t0) REVERT: C 269 GLU cc_start: 0.8804 (pm20) cc_final: 0.8297 (pm20) REVERT: C 306 MET cc_start: 0.8990 (tpp) cc_final: 0.8718 (tpt) REVERT: C 376 ARG cc_start: 0.8282 (tmt170) cc_final: 0.8024 (ttt-90) REVERT: C 406 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.5516 (p90) REVERT: D 154 GLU cc_start: 0.8232 (tp30) cc_final: 0.7949 (tp30) REVERT: D 269 GLU cc_start: 0.8026 (pp20) cc_final: 0.7797 (pp20) REVERT: D 332 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8778 (mm) REVERT: D 447 ASP cc_start: 0.7832 (p0) cc_final: 0.7280 (p0) REVERT: D 452 MET cc_start: 0.8547 (mtp) cc_final: 0.8304 (mtp) outliers start: 26 outliers final: 21 residues processed: 273 average time/residue: 0.1637 time to fit residues: 65.0603 Evaluate side-chains 261 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 520 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 0.0670 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: