Starting phenix.real_space_refine on Thu Feb 15 08:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhm_27436/02_2024/8dhm_27436_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhm_27436/02_2024/8dhm_27436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhm_27436/02_2024/8dhm_27436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhm_27436/02_2024/8dhm_27436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhm_27436/02_2024/8dhm_27436_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dhm_27436/02_2024/8dhm_27436_trim_updated.pdb" } resolution = 2.73 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 S 38 5.16 5 C 3759 2.51 5 N 940 2.21 5 O 1057 1.98 5 H 5900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11698 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' K': 2, '4AP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Time building chain proxies: 5.31, per 1000 atoms: 0.45 Number of scatterers: 11698 At special positions: 0 Unit cell: (104.55, 70.55, 80.75, 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) K 4 19.00 S 38 16.00 O 1057 8.00 N 940 7.00 C 3759 6.00 H 5900 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 83.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'B' and resid 34 through 56 removed outlier: 5.025A pdb=" N MET B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 64 through 101 removed outlier: 4.284A pdb=" N ARG B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 132 removed outlier: 3.773A pdb=" N PHE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 163 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 258 through 283 removed outlier: 5.135A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 299 through 333 removed outlier: 3.817A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.807A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 361 removed outlier: 4.093A pdb=" N GLY B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 369 through 404 removed outlier: 3.836A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 416 through 439 removed outlier: 5.257A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.560A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 460 removed outlier: 5.221A pdb=" N VAL B 445 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY B 446 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL B 455 " --> pdb=" O GLN B 452 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 462 through 475 Processing helix chain 'A' and resid 34 through 56 removed outlier: 5.025A pdb=" N MET A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 64 through 101 removed outlier: 4.285A pdb=" N ARG A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 132 removed outlier: 3.773A pdb=" N PHE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 138 through 163 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 258 through 283 removed outlier: 5.134A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 299 through 333 removed outlier: 3.817A pdb=" N THR A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.807A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 361 removed outlier: 4.093A pdb=" N GLY A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 369 through 404 removed outlier: 3.836A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 416 through 439 removed outlier: 5.256A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.560A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 460 removed outlier: 5.221A pdb=" N VAL A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 446 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL A 455 " --> pdb=" O GLN A 452 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 462 through 475 408 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 10.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5882 1.03 - 1.22: 18 1.22 - 1.42: 2386 1.42 - 1.61: 3393 1.61 - 1.81: 58 Bond restraints: 11737 Sorted by residual: bond pdb=" C4 4AP B 703 " pdb=" N4 4AP B 703 " ideal model delta sigma weight residual 1.324 1.445 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C4 4AP B 703 " pdb=" C5 4AP B 703 " ideal model delta sigma weight residual 1.417 1.349 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C3 4AP B 703 " pdb=" C4 4AP B 703 " ideal model delta sigma weight residual 1.416 1.350 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NH2 ARG A 97 " pdb="HH22 ARG A 97 " ideal model delta sigma weight residual 0.860 0.925 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" NH2 ARG B 97 " pdb="HH21 ARG B 97 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.28e+00 ... (remaining 11732 not shown) Histogram of bond angle deviations from ideal: 84.85 - 94.68: 5 94.68 - 104.51: 107 104.51 - 114.34: 14477 114.34 - 124.16: 5808 124.16 - 133.99: 875 Bond angle restraints: 21272 Sorted by residual: angle pdb=" CG ARG A 97 " pdb=" CD ARG A 97 " pdb=" HD3 ARG A 97 " ideal model delta sigma weight residual 109.00 85.27 23.73 3.00e+00 1.11e-01 6.26e+01 angle pdb=" NE ARG A 97 " pdb=" CD ARG A 97 " pdb=" HD3 ARG A 97 " ideal model delta sigma weight residual 108.00 84.85 23.15 3.00e+00 1.11e-01 5.95e+01 angle pdb=" CB ARG A 97 " pdb=" CG ARG A 97 " pdb=" CD ARG A 97 " ideal model delta sigma weight residual 111.30 93.97 17.33 2.30e+00 1.89e-01 5.67e+01 angle pdb=" CB ARG B 97 " pdb=" CG ARG B 97 " pdb=" CD ARG B 97 " ideal model delta sigma weight residual 111.30 93.99 17.31 2.30e+00 1.89e-01 5.67e+01 angle pdb=" CG ARG B 97 " pdb=" CD ARG B 97 " pdb=" NE ARG B 97 " ideal model delta sigma weight residual 112.00 126.07 -14.07 2.20e+00 2.07e-01 4.09e+01 ... (remaining 21267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4963 14.97 - 29.95: 402 29.95 - 44.92: 92 44.92 - 59.89: 59 59.89 - 74.87: 8 Dihedral angle restraints: 5524 sinusoidal: 2932 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLU B 282 " pdb=" C GLU B 282 " pdb=" N ASP B 283 " pdb=" CA ASP B 283 " ideal model delta harmonic sigma weight residual -180.00 -164.27 -15.73 0 5.00e+00 4.00e-02 9.89e+00 ... (remaining 5521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 555 0.030 - 0.061: 271 0.061 - 0.091: 106 0.091 - 0.121: 41 0.121 - 0.151: 5 Chirality restraints: 978 Sorted by residual: chirality pdb=" CB THR B 96 " pdb=" CA THR B 96 " pdb=" OG1 THR B 96 " pdb=" CG2 THR B 96 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CB THR A 96 " pdb=" CA THR A 96 " pdb=" OG1 THR A 96 " pdb=" CG2 THR A 96 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 60 " pdb=" N ILE B 60 " pdb=" C ILE B 60 " pdb=" CB ILE B 60 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 975 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 97 " -0.531 9.50e-02 1.11e+02 1.79e-01 4.23e+01 pdb=" NE ARG B 97 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG B 97 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 97 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG B 97 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG B 97 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG B 97 " -0.015 2.00e-02 2.50e+03 pdb="HH21 ARG B 97 " -0.007 2.00e-02 2.50e+03 pdb="HH22 ARG B 97 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 97 " 0.498 9.50e-02 1.11e+02 1.68e-01 3.81e+01 pdb=" NE ARG A 97 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 97 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 97 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 97 " 0.032 2.00e-02 2.50e+03 pdb="HH11 ARG A 97 " 0.012 2.00e-02 2.50e+03 pdb="HH12 ARG A 97 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 97 " -0.031 2.00e-02 2.50e+03 pdb="HH22 ARG A 97 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 452 " 0.005 2.00e-02 2.50e+03 1.57e-02 3.69e+00 pdb=" CD GLN A 452 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 452 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 452 " 0.029 2.00e-02 2.50e+03 pdb="HE21 GLN A 452 " -0.011 2.00e-02 2.50e+03 pdb="HE22 GLN A 452 " -0.007 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.29: 1925 2.29 - 3.00: 32647 3.00 - 3.71: 44760 3.71 - 4.43: 66982 4.43 - 5.14: 103983 Nonbonded interactions: 250297 Sorted by model distance: nonbonded pdb="HH12 ARG B 77 " pdb=" O HOH B 802 " model vdw 1.572 1.850 nonbonded pdb="HH12 ARG A 77 " pdb=" O HOH A 802 " model vdw 1.573 1.850 nonbonded pdb=" H GLN A 452 " pdb="HE21 GLN A 452 " model vdw 1.595 2.100 nonbonded pdb=" H GLN B 452 " pdb="HE22 GLN B 452 " model vdw 1.602 2.100 nonbonded pdb=" OD1 ASP B 106 " pdb=" H LEU B 109 " model vdw 1.745 1.850 ... (remaining 250292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 30 through 476 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 12.130 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 42.310 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.006 0.121 5837 Z= 0.398 Angle : 0.762 17.325 7954 Z= 0.412 Chirality : 0.042 0.151 978 Planarity : 0.011 0.219 975 Dihedral : 12.980 74.866 2034 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.65 % Allowed : 0.65 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.33), residues: 726 helix: 0.68 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.07 (0.65), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 394 HIS 0.007 0.002 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.013 0.002 TYR A 359 ARG 0.025 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 116 average time/residue: 2.5839 time to fit residues: 313.6587 Evaluate side-chains 62 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5837 Z= 0.268 Angle : 0.558 4.336 7954 Z= 0.292 Chirality : 0.037 0.134 978 Planarity : 0.005 0.055 975 Dihedral : 3.925 26.295 780 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.49 % Allowed : 9.22 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.33), residues: 726 helix: 1.65 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -0.07 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 394 HIS 0.006 0.001 HIS B 57 PHE 0.016 0.001 PHE B 99 TYR 0.010 0.001 TYR B 359 ARG 0.005 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 420 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7588 (t80) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 3.3447 time to fit residues: 215.5432 Evaluate side-chains 56 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain A residue 420 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5837 Z= 0.248 Angle : 0.510 4.223 7954 Z= 0.267 Chirality : 0.037 0.129 978 Planarity : 0.005 0.075 975 Dihedral : 3.850 24.165 780 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 8.41 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.33), residues: 726 helix: 2.11 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.15 (0.65), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 394 HIS 0.007 0.001 HIS B 57 PHE 0.011 0.001 PHE B 99 TYR 0.010 0.001 TYR A 359 ARG 0.003 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 57 average time/residue: 3.1477 time to fit residues: 186.9314 Evaluate side-chains 53 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.0170 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5837 Z= 0.202 Angle : 0.508 7.832 7954 Z= 0.260 Chirality : 0.036 0.134 978 Planarity : 0.004 0.041 975 Dihedral : 3.764 23.676 780 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.16 % Allowed : 9.06 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.33), residues: 726 helix: 2.35 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.44 (0.67), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 394 HIS 0.004 0.001 HIS B 57 PHE 0.018 0.001 PHE A 365 TYR 0.008 0.001 TYR B 359 ARG 0.005 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 3.0200 time to fit residues: 173.6241 Evaluate side-chains 52 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5837 Z= 0.201 Angle : 0.508 8.071 7954 Z= 0.259 Chirality : 0.036 0.126 978 Planarity : 0.004 0.041 975 Dihedral : 3.704 23.182 780 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.81 % Allowed : 9.06 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.33), residues: 726 helix: 2.44 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 0.62 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE B 99 TYR 0.008 0.001 TYR B 359 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: B 420 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7593 (t80) outliers start: 5 outliers final: 0 residues processed: 56 average time/residue: 2.7798 time to fit residues: 163.1917 Evaluate side-chains 54 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5837 Z= 0.241 Angle : 0.513 8.213 7954 Z= 0.264 Chirality : 0.036 0.129 978 Planarity : 0.004 0.041 975 Dihedral : 3.712 23.435 780 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.16 % Allowed : 10.03 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.33), residues: 726 helix: 2.49 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 0.63 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.020 0.001 PHE A 365 TYR 0.009 0.001 TYR B 359 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 3.0112 time to fit residues: 169.9111 Evaluate side-chains 53 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5837 Z= 0.257 Angle : 0.524 8.868 7954 Z= 0.268 Chirality : 0.037 0.124 978 Planarity : 0.004 0.038 975 Dihedral : 3.689 23.424 780 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.49 % Allowed : 10.68 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.33), residues: 726 helix: 2.51 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 0.65 (0.68), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.001 TYR B 359 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.974 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 2.8397 time to fit residues: 148.7983 Evaluate side-chains 51 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5837 Z= 0.239 Angle : 0.524 9.195 7954 Z= 0.267 Chirality : 0.036 0.125 978 Planarity : 0.004 0.036 975 Dihedral : 3.674 23.386 780 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.32 % Allowed : 11.17 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.33), residues: 726 helix: 2.56 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.76 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.019 0.001 PHE B 365 TYR 0.009 0.001 TYR B 359 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.863 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 2.4926 time to fit residues: 131.3032 Evaluate side-chains 50 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5837 Z= 0.195 Angle : 0.517 9.388 7954 Z= 0.263 Chirality : 0.036 0.125 978 Planarity : 0.004 0.035 975 Dihedral : 3.633 23.170 780 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.33), residues: 726 helix: 2.66 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.79 (0.69), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 394 HIS 0.003 0.001 HIS B 328 PHE 0.012 0.001 PHE B 99 TYR 0.009 0.001 TYR A 359 ARG 0.002 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.908 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 2.6700 time to fit residues: 138.3725 Evaluate side-chains 48 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5837 Z= 0.227 Angle : 0.526 9.697 7954 Z= 0.268 Chirality : 0.036 0.127 978 Planarity : 0.004 0.036 975 Dihedral : 3.629 22.981 780 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.33), residues: 726 helix: 2.68 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.73 (0.68), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 394 HIS 0.004 0.001 HIS B 328 PHE 0.025 0.001 PHE B 365 TYR 0.010 0.001 TYR A 359 ARG 0.002 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.911 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 2.6683 time to fit residues: 131.8972 Evaluate side-chains 47 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074065 restraints weight = 27874.167| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.22 r_work: 0.2909 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5837 Z= 0.233 Angle : 0.529 9.658 7954 Z= 0.271 Chirality : 0.036 0.125 978 Planarity : 0.004 0.036 975 Dihedral : 3.639 23.124 780 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.33), residues: 726 helix: 2.67 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 0.62 (0.68), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 394 HIS 0.004 0.001 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.001 TYR A 359 ARG 0.002 0.000 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.38 seconds wall clock time: 80 minutes 35.52 seconds (4835.52 seconds total)