Starting phenix.real_space_refine on Sat Apr 6 05:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/04_2024/7zki_14763_updated.pdb" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 38 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 80 5.49 5 Mg 1 5.21 5 S 8 5.16 5 C 4232 2.51 5 N 1251 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 GLU 29": "OE1" <-> "OE2" Residue "6 GLU 42": "OE1" <-> "OE2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 62": "NH1" <-> "NH2" Residue "6 ASP 92": "OD1" <-> "OD2" Residue "7 GLU 48": "OE1" <-> "OE2" Residue "7 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 302": "OD1" <-> "OD2" Residue "7 GLU 347": "OE1" <-> "OE2" Residue "7 ASP 363": "OD1" <-> "OD2" Residue "7 GLU 379": "OE1" <-> "OE2" Residue "7 ARG 383": "NH1" <-> "NH2" Residue "7 GLU 397": "OE1" <-> "OE2" Residue "7 GLU 423": "OE1" <-> "OE2" Residue "7 GLU 424": "OE1" <-> "OE2" Residue "7 PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7120 Number of models: 1 Model: "" Number of chains: 5 Chain: "4" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "7" Number of atoms: 4684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4684 Classifications: {'peptide': 595} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 567} Chain: "4" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.46, per 1000 atoms: 0.63 Number of scatterers: 7120 At special positions: 0 Unit cell: (126.42, 92.88, 147.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 80 15.00 Mg 1 11.99 O 1548 8.00 N 1251 7.00 C 4232 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 991.0 milliseconds 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 7 sheets defined 31.7% alpha, 19.6% beta 22 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain '6' and resid 53 through 56 No H-bonds generated for 'chain '6' and resid 53 through 56' Processing helix chain '6' and resid 88 through 97 Processing helix chain '6' and resid 102 through 106 Processing helix chain '7' and resid 20 through 28 removed outlier: 3.687A pdb=" N LEU 7 24 " --> pdb=" O LYS 7 20 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 39 No H-bonds generated for 'chain '7' and resid 37 through 39' Processing helix chain '7' and resid 51 through 57 Processing helix chain '7' and resid 60 through 64 Processing helix chain '7' and resid 86 through 95 Processing helix chain '7' and resid 111 through 122 Processing helix chain '7' and resid 134 through 136 No H-bonds generated for 'chain '7' and resid 134 through 136' Processing helix chain '7' and resid 148 through 154 removed outlier: 4.318A pdb=" N LYS 7 153 " --> pdb=" O LEU 7 149 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS 7 154 " --> pdb=" O MET 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 176 Processing helix chain '7' and resid 207 through 221 removed outlier: 3.673A pdb=" N SER 7 218 " --> pdb=" O ILE 7 214 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN 7 219 " --> pdb=" O ALA 7 215 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG 7 220 " --> pdb=" O GLY 7 216 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 7 221 " --> pdb=" O LEU 7 217 " (cutoff:3.500A) Processing helix chain '7' and resid 224 through 226 No H-bonds generated for 'chain '7' and resid 224 through 226' Processing helix chain '7' and resid 332 through 343 Processing helix chain '7' and resid 365 through 378 removed outlier: 3.794A pdb=" N LYS 7 378 " --> pdb=" O GLU 7 374 " (cutoff:3.500A) Processing helix chain '7' and resid 392 through 404 removed outlier: 4.260A pdb=" N GLU 7 404 " --> pdb=" O SER 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 406 through 408 No H-bonds generated for 'chain '7' and resid 406 through 408' Processing helix chain '7' and resid 420 through 429 Processing helix chain '7' and resid 439 through 459 removed outlier: 3.935A pdb=" N ASP 7 445 " --> pdb=" O LYS 7 441 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS 7 458 " --> pdb=" O GLU 7 454 " (cutoff:3.500A) Processing helix chain '7' and resid 461 through 464 No H-bonds generated for 'chain '7' and resid 461 through 464' Processing helix chain '7' and resid 559 through 567 Processing helix chain '7' and resid 575 through 588 Processing helix chain '7' and resid 593 through 597 Processing sheet with id= A, first strand: chain '6' and resid 67 through 71 removed outlier: 3.919A pdb=" N TYR 6 84 " --> pdb=" O ILE 6 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN 6 70 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE 6 82 " --> pdb=" O GLN 6 70 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY 6 80 " --> pdb=" O ILE 6 46 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG 6 48 " --> pdb=" O GLY 6 80 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE 6 82 " --> pdb=" O ARG 6 48 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG 6 50 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N TYR 6 84 " --> pdb=" O ARG 6 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN 6 30 " --> pdb=" O ASP 6 38 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG 6 40 " --> pdb=" O VAL 6 28 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL 6 28 " --> pdb=" O ARG 6 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 196 through 198 removed outlier: 9.360A pdb=" N VAL 7 197 " --> pdb=" O PHE 7 127 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL 7 129 " --> pdb=" O VAL 7 197 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA 7 99 " --> pdb=" O VAL 7 128 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA 7 130 " --> pdb=" O ALA 7 99 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU 7 101 " --> pdb=" O ALA 7 130 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ASN 7 132 " --> pdb=" O LEU 7 101 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL 7 103 " --> pdb=" O ASN 7 132 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '7' and resid 274 through 278 removed outlier: 3.560A pdb=" N THR 7 277 " --> pdb=" O ILE 7 266 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY 7 269 " --> pdb=" O PRO 7 325 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR 7 237 " --> pdb=" O ILE 7 255 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE 7 255 " --> pdb=" O THR 7 237 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '7' and resid 240 through 244 removed outlier: 3.600A pdb=" N GLU 7 240 " --> pdb=" O ASP 7 252 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY 7 248 " --> pdb=" O GLU 7 244 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '7' and resid 259 through 261 Processing sheet with id= F, first strand: chain '7' and resid 433 through 436 removed outlier: 6.586A pdb=" N ILE 7 411 " --> pdb=" O PHE 7 434 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLY 7 436 " --> pdb=" O ILE 7 411 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY 7 413 " --> pdb=" O GLY 7 436 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE 7 359 " --> pdb=" O LEU 7 412 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE 7 414 " --> pdb=" O ILE 7 359 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS 7 361 " --> pdb=" O PHE 7 414 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL 7 360 " --> pdb=" O ARG 7 383 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA 7 385 " --> pdb=" O VAL 7 360 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA 7 362 " --> pdb=" O ALA 7 385 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL 7 387 " --> pdb=" O ALA 7 362 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 552 through 554 removed outlier: 6.655A pdb=" N ARG 7 472 " --> pdb=" O VAL 7 493 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL 7 493 " --> pdb=" O ARG 7 472 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1916 1.34 - 1.45: 1514 1.45 - 1.57: 3799 1.57 - 1.69: 161 1.69 - 1.81: 12 Bond restraints: 7402 Sorted by residual: bond pdb=" C4 5MU 4 54 " pdb=" C5 5MU 4 54 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" N1 5MU 4 54 " pdb=" C6 5MU 4 54 " ideal model delta sigma weight residual 1.635 1.339 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C1' GNP 7 601 " pdb=" C2' GNP 7 601 " ideal model delta sigma weight residual 1.273 1.533 -0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C3' GNP 7 601 " pdb=" C4' GNP 7 601 " ideal model delta sigma weight residual 1.285 1.524 -0.239 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C5 5MU 4 54 " pdb=" C6 5MU 4 54 " ideal model delta sigma weight residual 1.155 1.387 -0.232 2.00e-02 2.50e+03 1.35e+02 ... (remaining 7397 not shown) Histogram of bond angle deviations from ideal: 94.44 - 102.50: 112 102.50 - 110.57: 2569 110.57 - 118.64: 3808 118.64 - 126.71: 3634 126.71 - 134.78: 260 Bond angle restraints: 10383 Sorted by residual: angle pdb=" O3' C 4 75 " pdb=" C3' C 4 75 " pdb=" C2' C 4 75 " ideal model delta sigma weight residual 109.50 119.43 -9.93 1.50e+00 4.44e-01 4.38e+01 angle pdb=" C4' C 4 75 " pdb=" C3' C 4 75 " pdb=" O3' C 4 75 " ideal model delta sigma weight residual 109.40 118.55 -9.15 1.50e+00 4.44e-01 3.73e+01 angle pdb=" N3B GNP 7 601 " pdb=" PB GNP 7 601 " pdb=" O1B GNP 7 601 " ideal model delta sigma weight residual 109.46 126.21 -16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N ARG 7 383 " pdb=" CA ARG 7 383 " pdb=" C ARG 7 383 " ideal model delta sigma weight residual 111.28 117.15 -5.87 1.09e+00 8.42e-01 2.90e+01 angle pdb=" N ARG 6 58 " pdb=" CA ARG 6 58 " pdb=" C ARG 6 58 " ideal model delta sigma weight residual 113.50 119.90 -6.40 1.23e+00 6.61e-01 2.71e+01 ... (remaining 10378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 4375 34.16 - 68.32: 219 68.32 - 102.48: 31 102.48 - 136.63: 1 136.63 - 170.79: 1 Dihedral angle restraints: 4627 sinusoidal: 2658 harmonic: 1969 Sorted by residual: dihedral pdb=" O4' C 4 17 " pdb=" C1' C 4 17 " pdb=" N1 C 4 17 " pdb=" C2 C 4 17 " ideal model delta sinusoidal sigma weight residual 200.00 90.29 109.71 1 1.50e+01 4.44e-03 5.71e+01 dihedral pdb=" C5' C 4 75 " pdb=" C4' C 4 75 " pdb=" C3' C 4 75 " pdb=" O3' C 4 75 " ideal model delta sinusoidal sigma weight residual 147.00 116.80 30.20 1 8.00e+00 1.56e-02 2.04e+01 dihedral pdb=" C4' C 4 75 " pdb=" C3' C 4 75 " pdb=" O3' C 4 75 " pdb=" P A 4 76 " ideal model delta sinusoidal sigma weight residual -110.00 60.79 -170.79 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 4624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1219 0.143 - 0.285: 8 0.285 - 0.428: 1 0.428 - 0.571: 0 0.571 - 0.713: 1 Chirality restraints: 1229 Sorted by residual: chirality pdb=" C3' C 4 75 " pdb=" C4' C 4 75 " pdb=" O3' C 4 75 " pdb=" C2' C 4 75 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA LYS 7 355 " pdb=" N LYS 7 355 " pdb=" C LYS 7 355 " pdb=" CB LYS 7 355 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ARG 6 58 " pdb=" N ARG 6 58 " pdb=" C ARG 6 58 " pdb=" CB ARG 6 58 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1226 not shown) Planarity restraints: 1038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP 7 601 " -0.459 2.00e-02 2.50e+03 5.80e-01 7.57e+03 pdb=" C2' GNP 7 601 " 0.609 2.00e-02 2.50e+03 pdb=" C3' GNP 7 601 " 0.276 2.00e-02 2.50e+03 pdb=" C4' GNP 7 601 " -0.201 2.00e-02 2.50e+03 pdb=" C5' GNP 7 601 " 0.885 2.00e-02 2.50e+03 pdb=" N9 GNP 7 601 " 0.031 2.00e-02 2.50e+03 pdb=" O2' GNP 7 601 " 0.479 2.00e-02 2.50e+03 pdb=" O3' GNP 7 601 " -0.749 2.00e-02 2.50e+03 pdb=" O4' GNP 7 601 " -0.870 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 4 54 " -0.035 2.00e-02 2.50e+03 5.60e-01 7.06e+03 pdb=" C4' 5MU 4 54 " -0.428 2.00e-02 2.50e+03 pdb=" O4' 5MU 4 54 " -0.592 2.00e-02 2.50e+03 pdb=" C3' 5MU 4 54 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 5MU 4 54 " 0.562 2.00e-02 2.50e+03 pdb=" C2' 5MU 4 54 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 5MU 4 54 " -0.907 2.00e-02 2.50e+03 pdb=" C1' 5MU 4 54 " -0.236 2.00e-02 2.50e+03 pdb=" N1 5MU 4 54 " 0.839 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 4 32 " -0.026 2.00e-02 2.50e+03 5.53e-01 6.87e+03 pdb=" C4' OMC 4 32 " -0.429 2.00e-02 2.50e+03 pdb=" O4' OMC 4 32 " -0.594 2.00e-02 2.50e+03 pdb=" C3' OMC 4 32 " 0.587 2.00e-02 2.50e+03 pdb=" O3' OMC 4 32 " 0.543 2.00e-02 2.50e+03 pdb=" C2' OMC 4 32 " 0.222 2.00e-02 2.50e+03 pdb=" O2' OMC 4 32 " -0.894 2.00e-02 2.50e+03 pdb=" C1' OMC 4 32 " -0.227 2.00e-02 2.50e+03 pdb=" N1 OMC 4 32 " 0.820 2.00e-02 2.50e+03 ... (remaining 1035 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.80: 1731 2.80 - 3.50: 9474 3.50 - 4.20: 17419 4.20 - 4.90: 27115 Nonbonded interactions: 55742 Sorted by model distance: nonbonded pdb=" O3' A 4 76 " pdb=" C MET 4 101 " model vdw 1.408 3.270 nonbonded pdb=" NZ LYS 7 286 " pdb=" OD2 ASP 7 299 " model vdw 2.012 2.520 nonbonded pdb=" O1G GNP 7 601 " pdb="MG MG 7 602 " model vdw 2.094 2.170 nonbonded pdb=" OG1 THR 7 21 " pdb="MG MG 7 602 " model vdw 2.112 2.170 nonbonded pdb=" OG1 THR 7 41 " pdb="MG MG 7 602 " model vdw 2.245 2.170 ... (remaining 55737 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 16.770 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 25.710 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 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 : 0.011 0.321 7402 Z= 0.652 Angle : 0.827 16.745 10383 Z= 0.374 Chirality : 0.048 0.713 1229 Planarity : 0.036 0.580 1038 Dihedral : 18.389 170.792 3357 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.17 % Allowed : 0.69 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: -0.08 (0.32), residues: 683 helix: 1.47 (0.38), residues: 212 sheet: -0.52 (0.39), residues: 159 loop : -0.80 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 65 HIS 0.002 0.001 HIS 7 249 PHE 0.015 0.001 PHE 7 174 TYR 0.010 0.001 TYR 7 440 ARG 0.004 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.707 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6641 (m-80) cc_final: 0.6278 (m-80) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.1800 time to fit residues: 16.1297 Evaluate side-chains 46 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7402 Z= 0.216 Angle : 0.936 18.389 10383 Z= 0.490 Chirality : 0.043 0.232 1229 Planarity : 0.008 0.122 1038 Dihedral : 19.899 174.200 1971 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.86 % Allowed : 6.69 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: -0.16 (0.31), residues: 683 helix: 1.59 (0.37), residues: 208 sheet: -0.69 (0.38), residues: 171 loop : -0.90 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 60 HIS 0.003 0.001 HIS 7 548 PHE 0.009 0.002 PHE 7 594 TYR 0.013 0.001 TYR 7 440 ARG 0.008 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.839 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6628 (m-80) cc_final: 0.6115 (m-80) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1576 time to fit residues: 11.8823 Evaluate side-chains 43 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 265 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 151 ASN ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7402 Z= 0.207 Angle : 0.908 17.043 10383 Z= 0.478 Chirality : 0.043 0.211 1229 Planarity : 0.008 0.119 1038 Dihedral : 19.843 177.004 1971 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 11.66 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: -0.28 (0.31), residues: 683 helix: 1.42 (0.37), residues: 206 sheet: -0.69 (0.39), residues: 163 loop : -0.94 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 7 65 HIS 0.003 0.001 HIS 7 546 PHE 0.011 0.002 PHE 7 594 TYR 0.014 0.002 TYR 7 440 ARG 0.005 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: 7 145 ASP cc_start: 0.8068 (t0) cc_final: 0.7712 (t70) REVERT: 7 203 TYR cc_start: 0.6660 (m-80) cc_final: 0.6167 (m-80) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1857 time to fit residues: 13.3639 Evaluate side-chains 47 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 128 VAL Chi-restraints excluded: chain 7 residue 211 LEU Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7402 Z= 0.126 Angle : 0.870 16.218 10383 Z= 0.467 Chirality : 0.041 0.210 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.760 175.703 1971 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.69 % Allowed : 14.92 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.32), residues: 683 helix: 1.62 (0.38), residues: 207 sheet: -0.50 (0.40), residues: 161 loop : -0.79 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 449 HIS 0.002 0.001 HIS 7 249 PHE 0.007 0.001 PHE 7 127 TYR 0.013 0.001 TYR 7 440 ARG 0.004 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.711 Fit side-chains REVERT: 7 133 LYS cc_start: 0.5983 (mmtt) cc_final: 0.5671 (mmtm) REVERT: 7 145 ASP cc_start: 0.7866 (t0) cc_final: 0.7441 (t70) REVERT: 7 203 TYR cc_start: 0.6698 (m-80) cc_final: 0.6313 (m-80) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1673 time to fit residues: 12.7896 Evaluate side-chains 47 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 498 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.0370 chunk 65 optimal weight: 0.0570 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.9178 ------------------------------------------------------------------------------- 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: 0.7317 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7402 Z= 0.130 Angle : 0.874 16.209 10383 Z= 0.464 Chirality : 0.041 0.232 1229 Planarity : 0.007 0.116 1038 Dihedral : 19.700 177.677 1971 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.20 % Allowed : 14.92 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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 (0.32), residues: 683 helix: 1.61 (0.38), residues: 207 sheet: -0.47 (0.40), residues: 161 loop : -0.72 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 7 449 HIS 0.001 0.001 HIS 7 249 PHE 0.007 0.001 PHE 7 127 TYR 0.013 0.001 TYR 7 440 ARG 0.003 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.715 Fit side-chains REVERT: 7 133 LYS cc_start: 0.6070 (mmtt) cc_final: 0.5683 (mmtm) REVERT: 7 145 ASP cc_start: 0.7898 (t0) cc_final: 0.7679 (t70) REVERT: 7 203 TYR cc_start: 0.6701 (m-80) cc_final: 0.6373 (m-80) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.1689 time to fit residues: 12.8501 Evaluate side-chains 46 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 498 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7335 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7402 Z= 0.148 Angle : 0.878 16.236 10383 Z= 0.466 Chirality : 0.041 0.203 1229 Planarity : 0.007 0.116 1038 Dihedral : 19.712 179.141 1971 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 15.44 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: 0.06 (0.32), residues: 683 helix: 1.68 (0.38), residues: 201 sheet: -0.47 (0.39), residues: 168 loop : -0.70 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 7 449 HIS 0.001 0.001 HIS 7 261 PHE 0.018 0.001 PHE 7 174 TYR 0.012 0.001 TYR 7 440 ARG 0.003 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.864 Fit side-chains REVERT: 7 145 ASP cc_start: 0.7951 (t0) cc_final: 0.7490 (t70) REVERT: 7 203 TYR cc_start: 0.6710 (m-80) cc_final: 0.6378 (m-80) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.1625 time to fit residues: 12.5642 Evaluate side-chains 49 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 6 residue 104 PHE Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 498 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7402 Z= 0.168 Angle : 0.890 16.300 10383 Z= 0.471 Chirality : 0.041 0.200 1229 Planarity : 0.007 0.116 1038 Dihedral : 19.728 179.797 1971 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.89 % Allowed : 16.12 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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 (0.32), residues: 683 helix: 1.57 (0.38), residues: 200 sheet: -0.47 (0.39), residues: 168 loop : -0.77 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 7 449 HIS 0.002 0.001 HIS 7 249 PHE 0.007 0.001 PHE 7 127 TYR 0.012 0.001 TYR 7 440 ARG 0.002 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.702 Fit side-chains REVERT: 7 145 ASP cc_start: 0.8001 (t0) cc_final: 0.7572 (t70) REVERT: 7 203 TYR cc_start: 0.6716 (m-80) cc_final: 0.6377 (m-80) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1355 time to fit residues: 10.6939 Evaluate side-chains 50 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 6 residue 104 PHE Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 439 ILE Chi-restraints excluded: chain 7 residue 498 ILE Chi-restraints excluded: chain 7 residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 65 optimal weight: 0.0870 chunk 69 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- 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: 0.7334 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7402 Z= 0.143 Angle : 0.876 16.207 10383 Z= 0.466 Chirality : 0.041 0.199 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.689 179.507 1971 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.89 % Allowed : 16.12 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: 0.07 (0.32), residues: 683 helix: 1.62 (0.38), residues: 200 sheet: -0.36 (0.40), residues: 161 loop : -0.69 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 449 HIS 0.001 0.001 HIS 7 249 PHE 0.007 0.001 PHE 7 127 TYR 0.013 0.001 TYR 7 440 ARG 0.002 0.000 ARG 6 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.734 Fit side-chains REVERT: 7 145 ASP cc_start: 0.8026 (t0) cc_final: 0.7599 (t70) REVERT: 7 203 TYR cc_start: 0.6669 (m-80) cc_final: 0.6381 (m-80) outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.1569 time to fit residues: 12.5185 Evaluate side-chains 49 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 439 ILE Chi-restraints excluded: chain 7 residue 498 ILE Chi-restraints excluded: chain 7 residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7402 Z= 0.252 Angle : 0.933 17.376 10383 Z= 0.489 Chirality : 0.044 0.341 1229 Planarity : 0.007 0.117 1038 Dihedral : 19.751 177.503 1971 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.89 % Allowed : 16.30 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: -0.24 (0.32), residues: 683 helix: 1.33 (0.38), residues: 200 sheet: -0.59 (0.39), residues: 170 loop : -0.83 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 7 595 HIS 0.003 0.001 HIS 7 546 PHE 0.009 0.001 PHE 7 127 TYR 0.010 0.001 TYR 7 440 ARG 0.004 0.000 ARG 6 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.667 Fit side-chains REVERT: 7 145 ASP cc_start: 0.8117 (t0) cc_final: 0.7696 (t70) REVERT: 7 203 TYR cc_start: 0.6624 (m-80) cc_final: 0.6227 (m-80) outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 0.1506 time to fit residues: 11.2260 Evaluate side-chains 45 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 98 LEU Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 439 ILE Chi-restraints excluded: chain 7 residue 498 ILE Chi-restraints excluded: chain 7 residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 68 optimal weight: 0.0570 chunk 59 optimal weight: 0.1980 chunk 6 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.0670 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7402 Z= 0.121 Angle : 0.881 16.167 10383 Z= 0.468 Chirality : 0.042 0.322 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.679 178.646 1971 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.37 % Allowed : 17.15 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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: 0.07 (0.32), residues: 683 helix: 1.48 (0.38), residues: 201 sheet: -0.26 (0.41), residues: 161 loop : -0.66 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 449 HIS 0.002 0.000 HIS 7 249 PHE 0.005 0.001 PHE 7 127 TYR 0.014 0.001 TYR 7 440 ARG 0.002 0.000 ARG 6 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1366 Ramachandran restraints generated. 683 Oldfield, 0 Emsley, 683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.637 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6657 (m-80) cc_final: 0.6449 (m-80) outliers start: 8 outliers final: 8 residues processed: 49 average time/residue: 0.1476 time to fit residues: 10.9947 Evaluate side-chains 48 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 101 THR Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 439 ILE Chi-restraints excluded: chain 7 residue 498 ILE Chi-restraints excluded: chain 7 residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.096173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081104 restraints weight = 26506.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082377 restraints weight = 26514.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082489 restraints weight = 18113.562| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7402 Z= 0.139 Angle : 0.892 16.154 10383 Z= 0.474 Chirality : 0.042 0.327 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.661 177.756 1971 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.72 % Allowed : 16.81 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.15 % 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 (0.32), residues: 683 helix: 1.50 (0.39), residues: 202 sheet: -0.11 (0.42), residues: 156 loop : -0.68 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 7 449 HIS 0.001 0.001 HIS 7 249 PHE 0.007 0.001 PHE 7 127 TYR 0.012 0.001 TYR 7 440 ARG 0.002 0.000 ARG 6 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1621.09 seconds wall clock time: 30 minutes 31.66 seconds (1831.66 seconds total)