Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:04:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dou_30800/11_2022/7dou_30800.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dou_30800/11_2022/7dou_30800.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/7dou_30800/11_2022/7dou_30800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dou_30800/11_2022/7dou_30800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dou_30800/11_2022/7dou_30800.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dou_30800/11_2022/7dou_30800.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "4 TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 24": "OD1" <-> "OD2" Residue "4 GLU 33": "OE1" <-> "OE2" Residue "4 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 80": "OD1" <-> "OD2" Residue "4 ASP 86": "OD1" <-> "OD2" Residue "4 GLU 121": "OE1" <-> "OE2" Residue "4 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 24": "OD1" <-> "OD2" Residue "5 GLU 33": "OE1" <-> "OE2" Residue "5 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 80": "OD1" <-> "OD2" Residue "5 ASP 86": "OD1" <-> "OD2" Residue "5 GLU 121": "OE1" <-> "OE2" Residue "5 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 24": "OD1" <-> "OD2" Residue "6 GLU 33": "OE1" <-> "OE2" Residue "6 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 80": "OD1" <-> "OD2" Residue "6 ASP 86": "OD1" <-> "OD2" Residue "6 GLU 121": "OE1" <-> "OE2" Residue "6 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2841 Number of models: 1 Model: "" Number of chains: 3 Chain: "4" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "5" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "6" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Time building chain proxies: 2.16, per 1000 atoms: 0.76 Number of scatterers: 2841 At special positions: 0 Unit cell: (73.08, 74.24, 73.08, 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 6 16.00 O 552 8.00 N 453 7.00 C 1830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 463.4 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 71.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '4' and resid 119 through 123 removed outlier: 14.736A pdb=" N LYS 4 2 " --> pdb=" O GLU 6 15 " (cutoff:3.500A) removed outlier: 11.732A pdb=" N GLU 6 15 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS 4 4 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS 6 13 " --> pdb=" O LYS 4 4 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS 6 107 " --> pdb=" O VAL 6 41 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL 6 41 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL 6 109 " --> pdb=" O LEU 6 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 6 39 " --> pdb=" O VAL 6 109 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG 6 111 " --> pdb=" O ILE 6 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE 6 37 " --> pdb=" O ARG 6 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 6 113 " --> pdb=" O ILE 6 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '4' and resid 119 through 123 removed outlier: 14.736A pdb=" N LYS 4 2 " --> pdb=" O GLU 6 15 " (cutoff:3.500A) removed outlier: 11.732A pdb=" N GLU 6 15 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS 4 4 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS 6 13 " --> pdb=" O LYS 4 4 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS 6 107 " --> pdb=" O VAL 6 41 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL 6 41 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL 6 109 " --> pdb=" O LEU 6 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 6 39 " --> pdb=" O VAL 6 109 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG 6 111 " --> pdb=" O ILE 6 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE 6 37 " --> pdb=" O ARG 6 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 6 113 " --> pdb=" O ILE 6 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 9 through 16 removed outlier: 6.640A pdb=" N LYS 4 107 " --> pdb=" O VAL 4 41 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL 4 41 " --> pdb=" O LYS 4 107 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL 4 109 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU 4 39 " --> pdb=" O VAL 4 109 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG 4 111 " --> pdb=" O ILE 4 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE 4 37 " --> pdb=" O ARG 4 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 4 113 " --> pdb=" O ILE 4 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '4' and resid 9 through 16 removed outlier: 6.640A pdb=" N LYS 4 107 " --> pdb=" O VAL 4 41 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL 4 41 " --> pdb=" O LYS 4 107 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL 4 109 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU 4 39 " --> pdb=" O VAL 4 109 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG 4 111 " --> pdb=" O ILE 4 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE 4 37 " --> pdb=" O ARG 4 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 4 113 " --> pdb=" O ILE 4 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 21 through 27 removed outlier: 6.576A pdb=" N VAL 4 89 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS 4 94 " --> pdb=" O HIS 4 49 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS 4 49 " --> pdb=" O LYS 4 94 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY 4 48 " --> pdb=" O PRO 4 69 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL 4 50 " --> pdb=" O THR 4 67 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR 4 67 " --> pdb=" O VAL 4 50 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL 4 52 " --> pdb=" O ILE 4 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain '5' and resid 9 through 16 removed outlier: 6.639A pdb=" N LYS 5 107 " --> pdb=" O VAL 5 41 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL 5 41 " --> pdb=" O LYS 5 107 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL 5 109 " --> pdb=" O LEU 5 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 5 39 " --> pdb=" O VAL 5 109 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG 5 111 " --> pdb=" O ILE 5 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE 5 37 " --> pdb=" O ARG 5 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 5 113 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 9 through 16 removed outlier: 6.639A pdb=" N LYS 5 107 " --> pdb=" O VAL 5 41 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL 5 41 " --> pdb=" O LYS 5 107 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL 5 109 " --> pdb=" O LEU 5 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU 5 39 " --> pdb=" O VAL 5 109 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG 5 111 " --> pdb=" O ILE 5 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE 5 37 " --> pdb=" O ARG 5 111 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU 5 113 " --> pdb=" O ILE 5 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 21 through 27 removed outlier: 6.576A pdb=" N VAL 5 89 " --> pdb=" O LEU 5 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS 5 94 " --> pdb=" O HIS 5 49 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS 5 49 " --> pdb=" O LYS 5 94 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY 5 48 " --> pdb=" O PRO 5 69 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL 5 50 " --> pdb=" O THR 5 67 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR 5 67 " --> pdb=" O VAL 5 50 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL 5 52 " --> pdb=" O ILE 5 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain '6' and resid 21 through 27 removed outlier: 6.576A pdb=" N VAL 6 89 " --> pdb=" O LEU 6 25 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS 6 94 " --> pdb=" O HIS 6 49 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS 6 49 " --> pdb=" O LYS 6 94 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY 6 48 " --> pdb=" O PRO 6 69 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL 6 50 " --> pdb=" O THR 6 67 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR 6 67 " --> pdb=" O VAL 6 50 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL 6 52 " --> pdb=" O ILE 6 65 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 366 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: 0.83 Time building geometry restraints manager: 1.20 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: 891 1.34 - 1.46: 461 1.46 - 1.57: 1528 1.57 - 1.69: 0 1.69 - 1.80: 9 Bond restraints: 2889 Sorted by residual: bond pdb=" CA LYS 5 60 " pdb=" CB LYS 5 60 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.42e-01 bond pdb=" CA LYS 4 60 " pdb=" CB LYS 4 60 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.37e-01 bond pdb=" CA LYS 6 60 " pdb=" C LYS 6 60 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.18e-01 bond pdb=" CA LYS 6 60 " pdb=" CB LYS 6 60 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.06e-01 bond pdb=" CA LYS 4 60 " pdb=" C LYS 4 60 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 4.92e-01 ... (remaining 2884 not shown) Histogram of bond angle deviations from ideal: 100.65 - 106.75: 72 106.75 - 112.86: 1607 112.86 - 118.96: 744 118.96 - 125.07: 1471 125.07 - 131.17: 21 Bond angle restraints: 3915 Sorted by residual: angle pdb=" N ASN 4 71 " pdb=" CA ASN 4 71 " pdb=" C ASN 4 71 " ideal model delta sigma weight residual 111.36 114.07 -2.71 1.09e+00 8.42e-01 6.20e+00 angle pdb=" N ASN 5 71 " pdb=" CA ASN 5 71 " pdb=" C ASN 5 71 " ideal model delta sigma weight residual 111.36 114.07 -2.71 1.09e+00 8.42e-01 6.16e+00 angle pdb=" N ASN 6 71 " pdb=" CA ASN 6 71 " pdb=" C ASN 6 71 " ideal model delta sigma weight residual 111.36 114.06 -2.70 1.09e+00 8.42e-01 6.13e+00 angle pdb=" N SER 4 101 " pdb=" CA SER 4 101 " pdb=" CB SER 4 101 " ideal model delta sigma weight residual 113.65 110.52 3.13 1.47e+00 4.63e-01 4.54e+00 angle pdb=" N SER 5 101 " pdb=" CA SER 5 101 " pdb=" CB SER 5 101 " ideal model delta sigma weight residual 113.65 110.53 3.12 1.47e+00 4.63e-01 4.50e+00 ... (remaining 3910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.25: 1491 12.25 - 24.50: 183 24.50 - 36.74: 69 36.74 - 48.99: 12 48.99 - 61.24: 3 Dihedral angle restraints: 1758 sinusoidal: 672 harmonic: 1086 Sorted by residual: dihedral pdb=" CA PHE 5 16 " pdb=" C PHE 5 16 " pdb=" N GLU 5 17 " pdb=" CA GLU 5 17 " ideal model delta harmonic sigma weight residual -180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE 4 16 " pdb=" C PHE 4 16 " pdb=" N GLU 4 17 " pdb=" CA GLU 4 17 " ideal model delta harmonic sigma weight residual 180.00 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE 6 16 " pdb=" C PHE 6 16 " pdb=" N GLU 6 17 " pdb=" CA GLU 6 17 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 1755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 220 0.024 - 0.048: 123 0.048 - 0.072: 59 0.072 - 0.096: 41 0.096 - 0.120: 28 Chirality restraints: 471 Sorted by residual: chirality pdb=" CA ILE 5 37 " pdb=" N ILE 5 37 " pdb=" C ILE 5 37 " pdb=" CB ILE 5 37 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE 4 37 " pdb=" N ILE 4 37 " pdb=" C ILE 4 37 " pdb=" CB ILE 4 37 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA ILE 6 37 " pdb=" N ILE 6 37 " pdb=" C ILE 6 37 " pdb=" CB ILE 6 37 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 468 not shown) Planarity restraints: 486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 5 68 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO 5 69 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO 5 69 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 5 69 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 4 68 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO 4 69 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO 4 69 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 4 69 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 6 68 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO 6 69 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO 6 69 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 6 69 " 0.030 5.00e-02 4.00e+02 ... (remaining 483 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 119 2.71 - 3.26: 2631 3.26 - 3.81: 4342 3.81 - 4.35: 5651 4.35 - 4.90: 9746 Nonbonded interactions: 22489 Sorted by model distance: nonbonded pdb=" OE2 GLU 5 40 " pdb=" NZ LYS 6 79 " model vdw 2.164 2.520 nonbonded pdb=" O SER 4 51 " pdb=" OH TYR 4 62 " model vdw 2.228 2.440 nonbonded pdb=" O SER 6 51 " pdb=" OH TYR 6 62 " model vdw 2.229 2.440 nonbonded pdb=" O SER 5 51 " pdb=" OH TYR 5 62 " model vdw 2.229 2.440 nonbonded pdb=" OE2 GLU 4 40 " pdb=" NZ LYS 5 79 " model vdw 2.278 2.520 ... (remaining 22484 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 '4' selection = chain '5' selection = chain '6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1830 2.51 5 N 453 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 21.600 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: 0.000 Extract box with map and model: 81.240 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.070 Process input model: 23.220 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.003 0.022 2889 Z= 0.217 Angle : 0.670 6.392 3915 Z= 0.373 Chirality : 0.046 0.120 471 Planarity : 0.005 0.054 486 Dihedral : 12.730 61.239 1062 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.00 % 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: -1.42 (0.43), residues: 366 helix: None (None), residues: 0 sheet: 0.19 (0.45), residues: 159 loop : -1.96 (0.37), residues: 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 1.1320 time to fit residues: 128.7315 Evaluate side-chains 76 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 2889 Z= 0.286 Angle : 0.652 6.281 3915 Z= 0.342 Chirality : 0.048 0.131 471 Planarity : 0.005 0.049 486 Dihedral : 5.745 22.582 396 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 5.66 % 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: -1.11 (0.43), residues: 366 helix: None (None), residues: 0 sheet: 0.69 (0.44), residues: 159 loop : -2.04 (0.38), residues: 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.346 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 91 average time/residue: 1.1082 time to fit residues: 103.4271 Evaluate side-chains 74 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0278 time to fit residues: 0.5032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 2889 Z= 0.290 Angle : 0.623 6.490 3915 Z= 0.330 Chirality : 0.048 0.131 471 Planarity : 0.005 0.046 486 Dihedral : 5.690 20.537 396 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 4.72 % 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: -1.03 (0.43), residues: 366 helix: None (None), residues: 0 sheet: 0.64 (0.44), residues: 159 loop : -1.88 (0.38), residues: 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.330 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 1.2022 time to fit residues: 99.8502 Evaluate side-chains 76 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.1560 time to fit residues: 2.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.8343 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 2889 Z= 0.239 Angle : 0.595 7.241 3915 Z= 0.313 Chirality : 0.048 0.128 471 Planarity : 0.004 0.046 486 Dihedral : 5.480 20.393 396 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 4.72 % 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: -1.02 (0.44), residues: 366 helix: None (None), residues: 0 sheet: 0.66 (0.44), residues: 159 loop : -1.88 (0.38), residues: 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.363 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 79 average time/residue: 1.1745 time to fit residues: 95.0935 Evaluate side-chains 80 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.7417 time to fit residues: 2.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 2889 Z= 0.318 Angle : 0.624 7.779 3915 Z= 0.329 Chirality : 0.048 0.132 471 Planarity : 0.004 0.045 486 Dihedral : 5.676 20.818 396 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 5.66 % 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: -1.04 (0.43), residues: 366 helix: None (None), residues: 0 sheet: 0.77 (0.44), residues: 156 loop : -1.98 (0.38), residues: 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.363 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 1.1368 time to fit residues: 96.7910 Evaluate side-chains 80 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1028 time to fit residues: 0.7449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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: 0.8353 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 2889 Z= 0.296 Angle : 0.641 8.392 3915 Z= 0.334 Chirality : 0.049 0.145 471 Planarity : 0.004 0.043 486 Dihedral : 5.698 21.024 396 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 5.35 % 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: -1.01 (0.43), residues: 366 helix: None (None), residues: 0 sheet: 0.62 (0.43), residues: 162 loop : -1.86 (0.39), residues: 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.387 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 84 average time/residue: 1.1219 time to fit residues: 96.6196 Evaluate side-chains 79 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1041 time to fit residues: 0.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 2889 Z= 0.241 Angle : 0.612 8.729 3915 Z= 0.320 Chirality : 0.048 0.144 471 Planarity : 0.004 0.044 486 Dihedral : 5.564 20.606 396 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 5.03 % 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: -0.90 (0.44), residues: 366 helix: None (None), residues: 0 sheet: 0.72 (0.44), residues: 162 loop : -1.82 (0.39), residues: 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.369 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 78 average time/residue: 0.9942 time to fit residues: 79.8328 Evaluate side-chains 77 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.0956 time to fit residues: 0.9483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 2889 Z= 0.422 Angle : 0.696 9.247 3915 Z= 0.365 Chirality : 0.050 0.154 471 Planarity : 0.004 0.042 486 Dihedral : 5.956 21.450 396 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 5.03 % 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: -1.00 (0.42), residues: 366 helix: None (None), residues: 0 sheet: 1.42 (0.48), residues: 123 loop : -1.97 (0.34), residues: 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.405 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 76 average time/residue: 1.0631 time to fit residues: 83.0044 Evaluate side-chains 78 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.0882 time to fit residues: 1.0595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 2889 Z= 0.293 Angle : 0.641 8.840 3915 Z= 0.337 Chirality : 0.048 0.150 471 Planarity : 0.004 0.044 486 Dihedral : 5.760 21.896 396 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 4.40 % 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: -1.10 (0.42), residues: 366 helix: None (None), residues: 0 sheet: 0.81 (0.46), residues: 138 loop : -1.86 (0.36), residues: 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.378 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 1.1310 time to fit residues: 90.5118 Evaluate side-chains 75 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1757 time to fit residues: 0.8907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8351 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 2889 Z= 0.300 Angle : 0.656 8.669 3915 Z= 0.346 Chirality : 0.048 0.154 471 Planarity : 0.004 0.042 486 Dihedral : 5.684 20.101 396 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 2.20 % 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: -1.08 (0.42), residues: 366 helix: None (None), residues: 0 sheet: 0.80 (0.46), residues: 138 loop : -1.82 (0.36), residues: 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.280 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 1.0339 time to fit residues: 78.6608 Evaluate side-chains 72 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.118854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089186 restraints weight = 4762.576| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.49 r_work: 0.3088 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work: 0.3062 rms_B_bonded: 2.28 restraints_weight: 0.1250 r_work: 0.3047 rms_B_bonded: 2.39 restraints_weight: 0.0625 r_work: 0.3031 rms_B_bonded: 2.57 restraints_weight: 0.0312 r_work: 0.3013 rms_B_bonded: 2.81 restraints_weight: 0.0156 r_work: 0.2992 rms_B_bonded: 3.13 restraints_weight: 0.0078 r_work: 0.2968 rms_B_bonded: 3.54 restraints_weight: 0.0039 r_work: 0.2941 rms_B_bonded: 4.08 restraints_weight: 0.0020 r_work: 0.2909 rms_B_bonded: 4.76 restraints_weight: 0.0010 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 2889 Z= 0.312 Angle : 0.655 8.650 3915 Z= 0.345 Chirality : 0.049 0.153 471 Planarity : 0.004 0.042 486 Dihedral : 5.724 20.785 396 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 2.83 % 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: -0.98 (0.42), residues: 366 helix: None (None), residues: 0 sheet: 1.37 (0.47), residues: 123 loop : -1.91 (0.35), residues: 243 =============================================================================== Job complete usr+sys time: 2625.21 seconds wall clock time: 47 minutes 20.76 seconds (2840.76 seconds total)