Starting phenix.real_space_refine on Thu Jan 18 01:19:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_2024/7zki_14763_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_2024/7zki_14763.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_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_14763/01_2024/7zki_14763_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_2024/7zki_14763_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_2024/7zki_14763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_2024/7zki_14763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_2024/7zki_14763_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zki_14763/01_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-1.21-5211/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: 4.85, per 1000 atoms: 0.68 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: 3.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.12 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: 2.64 Time building geometry restraints manager: 3.91 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: 4350 34.16 - 68.32: 208 68.32 - 102.48: 31 102.48 - 136.63: 1 136.63 - 170.79: 1 Dihedral angle restraints: 4591 sinusoidal: 2622 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 4588 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: 5.260 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: 17.070 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.610 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.130 ------------------------------------------------------------------------------- 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 : 18.129 170.792 3321 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 : 0.802 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: 0.1762 time to fit residues: 15.4136 Evaluate side-chains 46 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 0.7336 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7402 Z= 0.219 Angle : 0.944 18.449 10383 Z= 0.495 Chirality : 0.043 0.226 1229 Planarity : 0.008 0.120 1038 Dihedral : 19.566 173.887 1935 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.86 % Allowed : 7.03 % Favored : 92.11 % 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: -0.18 (0.31), residues: 683 helix: 1.58 (0.37), residues: 208 sheet: -0.70 (0.38), residues: 171 loop : -0.91 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 60 HIS 0.002 0.001 HIS 7 548 PHE 0.009 0.002 PHE 7 594 TYR 0.013 0.002 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 52 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.768 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6631 (m-80) cc_final: 0.6115 (m-80) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1547 time to fit residues: 11.9581 Evaluate side-chains 44 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7350 moved from start: 0.1583 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= 0.186 Angle : 0.896 16.403 10383 Z= 0.474 Chirality : 0.042 0.212 1229 Planarity : 0.007 0.119 1038 Dihedral : 19.416 175.765 1935 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.03 % Allowed : 10.98 % Favored : 87.99 % 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: -0.15 (0.32), residues: 683 helix: 1.55 (0.37), residues: 206 sheet: -0.64 (0.40), residues: 163 loop : -0.87 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 7 65 HIS 0.002 0.001 HIS 7 546 PHE 0.010 0.001 PHE 7 594 TYR 0.013 0.001 TYR 7 440 ARG 0.006 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 51 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.778 Fit side-chains REVERT: 7 133 LYS cc_start: 0.5969 (mmtt) cc_final: 0.5684 (mmtm) REVERT: 7 145 ASP cc_start: 0.7942 (t0) cc_final: 0.7557 (t70) REVERT: 7 203 TYR cc_start: 0.6657 (m-80) cc_final: 0.6163 (m-80) outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.1622 time to fit residues: 11.8582 Evaluate side-chains 49 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 44 ILE Chi-restraints excluded: chain 7 residue 53 VAL Chi-restraints excluded: chain 7 residue 211 LEU Chi-restraints excluded: chain 7 residue 265 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7311 moved from start: 0.1659 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= 0.128 Angle : 0.871 16.201 10383 Z= 0.466 Chirality : 0.041 0.209 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.343 175.652 1935 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.03 % Allowed : 13.55 % Favored : 85.42 % 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: 0.03 (0.32), residues: 683 helix: 1.65 (0.38), residues: 207 sheet: -0.48 (0.40), residues: 161 loop : -0.78 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.004 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 57 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: 7 133 LYS cc_start: 0.5886 (mmtt) cc_final: 0.5633 (mmtm) REVERT: 7 145 ASP cc_start: 0.7834 (t0) cc_final: 0.7605 (t70) REVERT: 7 203 TYR cc_start: 0.6685 (m-80) cc_final: 0.6306 (m-80) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.1653 time to fit residues: 13.2230 Evaluate side-chains 50 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 265 THR Chi-restraints excluded: chain 7 residue 326 VAL 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: 0.9980 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 0.0010 chunk 18 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7402 Z= 0.263 Angle : 0.941 17.832 10383 Z= 0.492 Chirality : 0.044 0.214 1229 Planarity : 0.008 0.119 1038 Dihedral : 19.442 179.966 1935 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.23 % Allowed : 14.75 % 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: -0.45 (0.32), residues: 683 helix: 1.27 (0.37), residues: 206 sheet: -0.83 (0.39), residues: 164 loop : -1.01 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 7 65 HIS 0.004 0.001 HIS 7 546 PHE 0.011 0.002 PHE 7 127 TYR 0.011 0.002 TYR 7 440 ARG 0.003 0.001 ARG 6 57 *********************** 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: 13 poor density : 40 time to evaluate : 0.901 Fit side-chains REVERT: 7 145 ASP cc_start: 0.8062 (t0) cc_final: 0.7737 (t70) REVERT: 7 203 TYR cc_start: 0.6572 (m-80) cc_final: 0.6063 (m-80) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.1632 time to fit residues: 12.0019 Evaluate side-chains 44 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 53 VAL Chi-restraints excluded: chain 7 residue 265 THR Chi-restraints excluded: chain 7 residue 326 VAL Chi-restraints excluded: chain 7 residue 489 VAL 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: 0.0270 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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: 0.7311 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7402 Z= 0.117 Angle : 0.873 16.209 10383 Z= 0.467 Chirality : 0.041 0.206 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.364 177.774 1935 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.86 % Allowed : 16.30 % Favored : 82.85 % 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: 0.05 (0.32), residues: 683 helix: 1.70 (0.38), residues: 200 sheet: -0.48 (0.40), residues: 161 loop : -0.72 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 7 449 HIS 0.001 0.000 HIS 7 249 PHE 0.007 0.001 PHE 7 127 TYR 0.014 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 49 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: 7 145 ASP cc_start: 0.7919 (t0) cc_final: 0.7446 (t70) REVERT: 7 203 TYR cc_start: 0.6729 (m-80) cc_final: 0.6417 (m-80) REVERT: 4 101 MET cc_start: 0.6565 (mmt) cc_final: 0.5928 (mmt) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1706 time to fit residues: 12.3325 Evaluate side-chains 43 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 10 ILE Chi-restraints excluded: chain 7 residue 44 ILE 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: 1.9990 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7402 Z= 0.217 Angle : 0.910 16.323 10383 Z= 0.480 Chirality : 0.042 0.202 1229 Planarity : 0.007 0.117 1038 Dihedral : 19.416 179.109 1935 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.72 % Allowed : 15.61 % Favored : 82.68 % 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: -0.15 (0.32), residues: 683 helix: 1.55 (0.37), residues: 200 sheet: -0.66 (0.39), residues: 170 loop : -0.81 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 60 HIS 0.002 0.001 HIS 7 546 PHE 0.014 0.002 PHE 7 174 TYR 0.011 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 50 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.740 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6653 (m-80) cc_final: 0.6253 (m-80) REVERT: 4 101 MET cc_start: 0.6759 (mmt) cc_final: 0.6365 (mmt) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.1631 time to fit residues: 11.6048 Evaluate side-chains 45 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain 7 residue 498 ILE 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: 1.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7402 Z= 0.149 Angle : 0.889 16.275 10383 Z= 0.472 Chirality : 0.041 0.200 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.398 179.575 1935 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.72 % Allowed : 16.12 % Favored : 82.16 % 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: -0.05 (0.32), residues: 683 helix: 1.56 (0.38), residues: 200 sheet: -0.49 (0.40), residues: 161 loop : -0.76 (0.34), residues: 322 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 0.002 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 50 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.744 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6691 (m-80) cc_final: 0.6358 (m-80) REVERT: 4 101 MET cc_start: 0.6662 (mmt) cc_final: 0.6137 (mmt) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.1663 time to fit residues: 12.0465 Evaluate side-chains 47 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 0.0010 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7402 Z= 0.141 Angle : 0.878 16.261 10383 Z= 0.468 Chirality : 0.041 0.198 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.358 178.637 1935 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.54 % Allowed : 16.64 % 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: 0.07 (0.32), residues: 683 helix: 1.64 (0.38), residues: 200 sheet: -0.40 (0.41), residues: 161 loop : -0.69 (0.34), residues: 322 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 0.013 0.001 TYR 7 440 ARG 0.002 0.000 ARG 6 50 *********************** 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 52 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.666 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6673 (m-80) cc_final: 0.6379 (m-80) outliers start: 9 outliers final: 9 residues processed: 51 average time/residue: 0.1636 time to fit residues: 12.4422 Evaluate side-chains 47 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 326 VAL Chi-restraints excluded: chain 7 residue 421 ASP 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: 6.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.0020 chunk 68 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 0.0070 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0012 ------------------------------------------------------------------------------- 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: 0.7329 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7402 Z= 0.141 Angle : 0.882 16.124 10383 Z= 0.470 Chirality : 0.041 0.196 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.310 178.266 1935 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.54 % Allowed : 16.98 % 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: 0.02 (0.32), residues: 683 helix: 1.59 (0.38), residues: 201 sheet: -0.36 (0.41), residues: 161 loop : -0.76 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 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 48 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.771 Fit side-chains REVERT: 7 203 TYR cc_start: 0.6624 (m-80) cc_final: 0.6313 (m-80) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.1708 time to fit residues: 11.8192 Evaluate side-chains 47 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.096417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081226 restraints weight = 26602.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.082783 restraints weight = 24939.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.082745 restraints weight = 15984.980| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7402 Z= 0.130 Angle : 0.872 16.414 10383 Z= 0.466 Chirality : 0.040 0.195 1229 Planarity : 0.007 0.115 1038 Dihedral : 19.248 177.943 1935 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.12 (0.32), residues: 683 helix: 1.59 (0.38), residues: 203 sheet: -0.23 (0.42), residues: 158 loop : -0.70 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 7 449 HIS 0.001 0.000 HIS 7 548 PHE 0.007 0.001 PHE 7 127 TYR 0.013 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: 1576.30 seconds wall clock time: 29 minutes 37.47 seconds (1777.47 seconds total)