Starting phenix.real_space_refine on Thu Dec 7 20:31:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7o_15222/12_2023/8a7o_15222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7o_15222/12_2023/8a7o_15222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7o_15222/12_2023/8a7o_15222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7o_15222/12_2023/8a7o_15222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7o_15222/12_2023/8a7o_15222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7o_15222/12_2023/8a7o_15222.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2790 2.51 5 N 714 2.21 5 O 840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "B" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "C" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "D" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "E" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "F" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 727 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Time building chain proxies: 2.85, per 1000 atoms: 0.65 Number of scatterers: 4362 At special positions: 0 Unit cell: (122.84, 109.56, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 840 8.00 N 714 7.00 C 2790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " distance=2.03 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: 1.43 Conformation dependent library (CDL) restraints added in 845.4 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.494A pdb=" N GLN A 8 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER C 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN C 8 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER E 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.222A pdb=" N TYR A 26 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C 26 " --> pdb=" O VAL E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.868A pdb=" N ASP C 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP E 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 46 removed outlier: 7.032A pdb=" N ILE C 46 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 46 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.660A pdb=" N VAL A 49 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 49 " --> pdb=" O GLU E 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.346A pdb=" N SER A 61 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU C 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR A 63 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR C 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 65 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER C 61 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU E 64 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 63 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N TYR E 66 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 65 " --> pdb=" O TYR E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AB1, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 88 removed outlier: 6.528A pdb=" N ARG A 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS C 84 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A 83 " --> pdb=" O HIS C 84 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR C 86 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 85 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER C 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 87 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG C 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS E 84 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASN C 83 " --> pdb=" O HIS E 84 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR E 86 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 85 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N SER E 88 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 87 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.559A pdb=" N LYS A 91 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 91 " --> pdb=" O ILE E 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 7 through 12 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.947A pdb=" N ASN D 21 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F 21 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.919A pdb=" N ASP D 34 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP F 34 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 53 removed outlier: 9.168A pdb=" N LYS B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N HIS D 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 50 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP D 53 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 52 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LYS D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N HIS F 51 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 50 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ASP F 53 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 59 through 66 removed outlier: 7.096A pdb=" N TYR D 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 64 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU D 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B 66 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR F 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU D 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU F 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR D 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 73 through 78 Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.639A pdb=" N VAL B 82 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 82 " --> pdb=" O ASN F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.475A pdb=" N LEU B 87 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 87 " --> pdb=" O SER F 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 91 through 92 removed outlier: 6.740A pdb=" N LYS B 91 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS D 91 " --> pdb=" O ILE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 86 hydrogen bonds defined for protein. 258 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: 1.11 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1392 1.34 - 1.46: 977 1.46 - 1.58: 2089 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4482 Sorted by residual: bond pdb=" C THR C 71 " pdb=" N PRO C 72 " ideal model delta sigma weight residual 1.333 1.342 -0.009 1.20e-02 6.94e+03 5.69e-01 bond pdb=" C ASN F 42 " pdb=" N GLY F 43 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.41e-02 5.03e+03 5.30e-01 bond pdb=" C TYR F 78 " pdb=" N ALA F 79 " ideal model delta sigma weight residual 1.333 1.342 -0.009 1.30e-02 5.92e+03 5.09e-01 bond pdb=" C THR A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.333 1.341 -0.008 1.20e-02 6.94e+03 5.00e-01 bond pdb=" C ASN D 42 " pdb=" N GLY D 43 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.41e-02 5.03e+03 4.77e-01 ... (remaining 4477 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 180 107.46 - 114.10: 2471 114.10 - 120.73: 1748 120.73 - 127.36: 1616 127.36 - 133.99: 57 Bond angle restraints: 6072 Sorted by residual: angle pdb=" N LYS D 48 " pdb=" CA LYS D 48 " pdb=" C LYS D 48 " ideal model delta sigma weight residual 108.13 111.44 -3.31 1.72e+00 3.38e-01 3.69e+00 angle pdb=" N LYS F 48 " pdb=" CA LYS F 48 " pdb=" C LYS F 48 " ideal model delta sigma weight residual 108.13 111.41 -3.28 1.72e+00 3.38e-01 3.64e+00 angle pdb=" N LYS B 48 " pdb=" CA LYS B 48 " pdb=" C LYS B 48 " ideal model delta sigma weight residual 108.13 111.40 -3.27 1.72e+00 3.38e-01 3.61e+00 angle pdb=" C LYS F 19 " pdb=" N SER F 20 " pdb=" CA SER F 20 " ideal model delta sigma weight residual 121.62 118.42 3.20 1.83e+00 2.99e-01 3.07e+00 angle pdb=" C LYS B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta sigma weight residual 121.62 118.46 3.16 1.83e+00 2.99e-01 2.98e+00 ... (remaining 6067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.02: 2477 13.02 - 26.03: 142 26.03 - 39.05: 24 39.05 - 52.07: 15 52.07 - 65.08: 18 Dihedral angle restraints: 2676 sinusoidal: 1098 harmonic: 1578 Sorted by residual: dihedral pdb=" CA ARG D 12 " pdb=" CB ARG D 12 " pdb=" CG ARG D 12 " pdb=" CD ARG D 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.74 54.26 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA ARG F 12 " pdb=" CB ARG F 12 " pdb=" CG ARG F 12 " pdb=" CD ARG F 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.80 54.20 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CA ARG B 12 " pdb=" CB ARG B 12 " pdb=" CG ARG B 12 " pdb=" CD ARG B 12 " ideal model delta sinusoidal sigma weight residual 180.00 125.83 54.17 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 2673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 303 0.026 - 0.052: 226 0.052 - 0.078: 53 0.078 - 0.104: 19 0.104 - 0.130: 41 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA PRO F 14 " pdb=" N PRO F 14 " pdb=" C PRO F 14 " pdb=" CB PRO F 14 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 639 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 13 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO D 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 13 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 14 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 13 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO F 14 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " 0.025 5.00e-02 4.00e+02 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 1549 2.91 - 3.41: 3409 3.41 - 3.91: 7113 3.91 - 4.40: 6917 4.40 - 4.90: 12418 Nonbonded interactions: 31406 Sorted by model distance: nonbonded pdb=" O LYS B 58 " pdb=" N LYS D 58 " model vdw 2.418 2.520 nonbonded pdb=" O LYS D 58 " pdb=" N LYS F 58 " model vdw 2.419 2.520 nonbonded pdb=" OE2 GLU A 16 " pdb=" NH2 ARG A 81 " model vdw 2.595 2.520 nonbonded pdb=" OE2 GLU E 16 " pdb=" NH2 ARG E 81 " model vdw 2.595 2.520 nonbonded pdb=" OE2 GLU C 16 " pdb=" NH2 ARG C 81 " model vdw 2.596 2.520 ... (remaining 31401 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.610 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.000 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4482 Z= 0.159 Angle : 0.549 5.776 6072 Z= 0.316 Chirality : 0.045 0.130 642 Planarity : 0.004 0.044 780 Dihedral : 11.280 65.084 1638 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 60 HIS 0.004 0.001 HIS E 13 PHE 0.008 0.001 PHE B 22 TYR 0.006 0.001 TYR E 63 ARG 0.001 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.7500 time to fit residues: 145.2780 Evaluate side-chains 41 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 13 HIS A 31 HIS A 42 ASN B 13 HIS B 89 GLN C 8 GLN C 13 HIS C 31 HIS C 42 ASN D 89 GLN E 8 GLN E 13 HIS E 42 ASN F 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4482 Z= 0.309 Angle : 0.624 7.766 6072 Z= 0.347 Chirality : 0.047 0.148 642 Planarity : 0.004 0.042 780 Dihedral : 4.893 16.851 576 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.01 % Allowed : 9.24 % Favored : 88.76 % 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: -3.61 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 60 HIS 0.005 0.001 HIS A 13 PHE 0.017 0.002 PHE D 22 TYR 0.014 0.002 TYR E 67 ARG 0.008 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.505 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 61 average time/residue: 1.9105 time to fit residues: 119.4574 Evaluate side-chains 46 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 50.0000 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 0.3980 chunk 43 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4482 Z= 0.305 Angle : 0.605 5.341 6072 Z= 0.336 Chirality : 0.047 0.142 642 Planarity : 0.004 0.040 780 Dihedral : 5.078 16.556 576 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.01 % Allowed : 10.84 % Favored : 87.15 % 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: -3.66 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 60 HIS 0.005 0.001 HIS A 13 PHE 0.017 0.002 PHE D 22 TYR 0.014 0.002 TYR E 67 ARG 0.003 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.561 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 1.9473 time to fit residues: 109.7916 Evaluate side-chains 44 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4482 Z= 0.322 Angle : 0.608 4.409 6072 Z= 0.337 Chirality : 0.047 0.142 642 Planarity : 0.004 0.036 780 Dihedral : 5.115 16.239 576 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.41 % Allowed : 11.45 % Favored : 87.15 % 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: -3.61 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 60 HIS 0.004 0.001 HIS B 31 PHE 0.017 0.002 PHE D 22 TYR 0.014 0.002 TYR E 67 ARG 0.003 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.501 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 48 average time/residue: 1.9176 time to fit residues: 94.6730 Evaluate side-chains 40 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- 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: 0.8647 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4482 Z= 0.411 Angle : 0.650 4.745 6072 Z= 0.363 Chirality : 0.048 0.142 642 Planarity : 0.004 0.037 780 Dihedral : 5.235 16.077 576 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.81 % Allowed : 11.85 % Favored : 86.35 % 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: -3.62 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.005 0.001 HIS F 31 PHE 0.018 0.002 PHE D 22 TYR 0.014 0.002 TYR A 66 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.525 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 47 average time/residue: 2.0725 time to fit residues: 99.9516 Evaluate side-chains 44 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.7111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- 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: 0.8610 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4482 Z= 0.250 Angle : 0.583 4.777 6072 Z= 0.321 Chirality : 0.046 0.136 642 Planarity : 0.003 0.034 780 Dihedral : 5.056 16.130 576 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.20 % Allowed : 13.25 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS D 31 PHE 0.019 0.002 PHE D 22 TYR 0.014 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 2.0052 time to fit residues: 96.6815 Evaluate side-chains 40 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 40.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4482 Z= 0.326 Angle : 0.622 6.046 6072 Z= 0.344 Chirality : 0.047 0.136 642 Planarity : 0.003 0.033 780 Dihedral : 5.108 15.504 576 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 13.86 % Favored : 84.74 % 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: -3.64 (0.28), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.017 0.002 PHE D 22 TYR 0.016 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.552 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 2.0272 time to fit residues: 95.6767 Evaluate side-chains 43 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.9033 time to fit residues: 2.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 0.0010 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- 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: 0.8603 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4482 Z= 0.238 Angle : 0.577 6.400 6072 Z= 0.318 Chirality : 0.046 0.133 642 Planarity : 0.003 0.032 780 Dihedral : 4.976 15.395 576 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.00 % Allowed : 14.26 % Favored : 84.74 % 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: -3.61 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS D 31 PHE 0.018 0.002 PHE D 22 TYR 0.015 0.002 TYR E 67 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.539 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 1.8959 time to fit residues: 93.5044 Evaluate side-chains 39 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 20.0000 chunk 13 optimal weight: 0.0040 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 overall best weight: 4.3598 ------------------------------------------------------------------------------- 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: 0.8602 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4482 Z= 0.236 Angle : 0.584 5.773 6072 Z= 0.320 Chirality : 0.046 0.131 642 Planarity : 0.003 0.031 780 Dihedral : 4.943 15.318 576 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.60 % Allowed : 15.46 % Favored : 83.94 % 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: -3.57 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 60 HIS 0.004 0.001 HIS B 31 PHE 0.017 0.002 PHE D 22 TYR 0.018 0.002 TYR E 67 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.534 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 1.8753 time to fit residues: 88.6230 Evaluate side-chains 43 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.8626 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4482 Z= 0.314 Angle : 0.610 7.308 6072 Z= 0.339 Chirality : 0.047 0.134 642 Planarity : 0.003 0.031 780 Dihedral : 5.057 15.293 576 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.60 % Allowed : 15.46 % Favored : 83.94 % 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: -3.61 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.017 0.002 PHE D 22 TYR 0.017 0.002 TYR E 67 ARG 0.003 0.000 ARG A 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.561 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 1.8888 time to fit residues: 89.2895 Evaluate side-chains 43 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.085185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.070599 restraints weight = 11415.539| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.28 r_work: 0.3465 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4482 Z= 0.321 Angle : 0.621 5.940 6072 Z= 0.343 Chirality : 0.047 0.134 642 Planarity : 0.003 0.031 780 Dihedral : 5.098 15.358 576 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.60 % Allowed : 16.06 % Favored : 83.33 % 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: -3.61 (0.29), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.001 HIS F 31 PHE 0.017 0.002 PHE D 22 TYR 0.017 0.002 TYR E 67 ARG 0.002 0.000 ARG A 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.92 seconds wall clock time: 36 minutes 47.25 seconds (2207.25 seconds total)