Starting phenix.real_space_refine on Wed Feb 14 17:48:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxt_15016/02_2024/7zxt_15016.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxt_15016/02_2024/7zxt_15016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxt_15016/02_2024/7zxt_15016.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxt_15016/02_2024/7zxt_15016.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxt_15016/02_2024/7zxt_15016.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxt_15016/02_2024/7zxt_15016.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 90 5.16 5 C 6534 2.51 5 N 1668 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9924 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1654 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1654 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "C" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1654 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "D" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1654 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1654 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "F" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1654 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 5.50, per 1000 atoms: 0.55 Number of scatterers: 9924 At special positions: 0 Unit cell: (105.294, 101.37, 91.56, 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 90 16.00 O 1632 8.00 N 1668 7.00 C 6534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " 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: 3.89 Conformation dependent library (CDL) restraints added in 1.7 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 72.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 23 through 42 removed outlier: 3.608A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 157 Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 23 through 42 removed outlier: 3.608A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 157 Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 23 through 42 removed outlier: 3.609A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 157 Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 23 through 42 removed outlier: 3.609A pdb=" N VAL D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 157 Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 23 through 42 removed outlier: 3.609A pdb=" N VAL E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 157 Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 23 through 42 removed outlier: 3.609A pdb=" N VAL F 27 " --> pdb=" O VAL F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 157 Processing helix chain 'F' and resid 183 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 4.039A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 180 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 4.038A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 180 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 4.039A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 180 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 4.039A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 180 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 4.038A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 180 " --> pdb=" O ILE E 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 4.038A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE F 180 " --> pdb=" O ILE F 52 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2235 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: 2.82 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3006 1.35 - 1.47: 2751 1.47 - 1.60: 4293 1.60 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 10182 Sorted by residual: bond pdb=" C THR B 86 " pdb=" N PRO B 87 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.64e+00 bond pdb=" C THR E 86 " pdb=" N PRO E 87 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.64e+00 bond pdb=" C THR F 86 " pdb=" N PRO F 87 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.62e+00 bond pdb=" C THR D 86 " pdb=" N PRO D 87 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.47e+00 bond pdb=" C THR C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.42e+00 ... (remaining 10177 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.04: 264 107.04 - 113.78: 5936 113.78 - 120.52: 3732 120.52 - 127.26: 3792 127.26 - 133.99: 136 Bond angle restraints: 13860 Sorted by residual: angle pdb=" N ILE A 20 " pdb=" CA ILE A 20 " pdb=" C ILE A 20 " ideal model delta sigma weight residual 112.12 108.02 4.10 8.40e-01 1.42e+00 2.38e+01 angle pdb=" N ILE D 20 " pdb=" CA ILE D 20 " pdb=" C ILE D 20 " ideal model delta sigma weight residual 112.12 108.06 4.06 8.40e-01 1.42e+00 2.34e+01 angle pdb=" N ILE E 20 " pdb=" CA ILE E 20 " pdb=" C ILE E 20 " ideal model delta sigma weight residual 112.12 108.06 4.06 8.40e-01 1.42e+00 2.34e+01 angle pdb=" N ILE C 20 " pdb=" CA ILE C 20 " pdb=" C ILE C 20 " ideal model delta sigma weight residual 112.12 108.07 4.05 8.40e-01 1.42e+00 2.33e+01 angle pdb=" N ILE F 20 " pdb=" CA ILE F 20 " pdb=" C ILE F 20 " ideal model delta sigma weight residual 112.12 108.07 4.05 8.40e-01 1.42e+00 2.33e+01 ... (remaining 13855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 5409 14.98 - 29.96: 440 29.96 - 44.94: 127 44.94 - 59.92: 12 59.92 - 74.90: 6 Dihedral angle restraints: 5994 sinusoidal: 2340 harmonic: 3654 Sorted by residual: dihedral pdb=" CA CYS E 179 " pdb=" C CYS E 179 " pdb=" N PHE E 180 " pdb=" CA PHE E 180 " ideal model delta harmonic sigma weight residual 180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA CYS B 179 " pdb=" C CYS B 179 " pdb=" N PHE B 180 " pdb=" CA PHE B 180 " ideal model delta harmonic sigma weight residual -180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA CYS F 179 " pdb=" C CYS F 179 " pdb=" N PHE F 180 " pdb=" CA PHE F 180 " ideal model delta harmonic sigma weight residual 180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 5991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1157 0.041 - 0.081: 399 0.081 - 0.122: 64 0.122 - 0.162: 6 0.162 - 0.203: 18 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL F 13 " pdb=" CA VAL F 13 " pdb=" CG1 VAL F 13 " pdb=" CG2 VAL F 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL D 13 " pdb=" CA VAL D 13 " pdb=" CG1 VAL D 13 " pdb=" CG2 VAL D 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL A 13 " pdb=" CA VAL A 13 " pdb=" CG1 VAL A 13 " pdb=" CG2 VAL A 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1641 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 183 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO F 184 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 183 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 184 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 184 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 184 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 183 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO C 184 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " -0.017 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 126 2.70 - 3.25: 10088 3.25 - 3.80: 16732 3.80 - 4.35: 19610 4.35 - 4.90: 33380 Nonbonded interactions: 79936 Sorted by model distance: nonbonded pdb=" O ILE E 71 " pdb=" OH TYR E 157 " model vdw 2.146 2.440 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 157 " model vdw 2.147 2.440 nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 157 " model vdw 2.147 2.440 nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 157 " model vdw 2.147 2.440 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 157 " model vdw 2.148 2.440 ... (remaining 79931 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: 3.180 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: 0.020 Extract box with map and model: 11.770 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.790 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 0.035 10182 Z= 0.193 Angle : 0.626 7.337 13860 Z= 0.363 Chirality : 0.043 0.203 1644 Planarity : 0.003 0.030 1662 Dihedral : 12.065 74.901 3564 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.47 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: 3.83 (0.24), residues: 1212 helix: 3.93 (0.15), residues: 876 sheet: 1.68 (0.55), residues: 60 loop : -2.43 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 44 HIS 0.002 0.000 HIS C 97 PHE 0.008 0.001 PHE E 51 TYR 0.007 0.001 TYR B 135 ARG 0.002 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.137 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 1.2563 time to fit residues: 320.5193 Evaluate side-chains 158 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 99 GLN D 97 HIS E 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10182 Z= 0.372 Angle : 0.640 9.567 13860 Z= 0.336 Chirality : 0.044 0.163 1644 Planarity : 0.004 0.031 1662 Dihedral : 4.525 31.597 1350 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.55 % Favored : 95.96 % Rotamer: Outliers : 3.33 % Allowed : 13.69 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: 3.49 (0.23), residues: 1212 helix: 3.80 (0.14), residues: 870 sheet: 0.35 (0.56), residues: 72 loop : -2.68 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 132 HIS 0.010 0.002 HIS B 123 PHE 0.011 0.002 PHE D 180 TYR 0.011 0.001 TYR B 151 ARG 0.003 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 1.170 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 183 average time/residue: 1.2870 time to fit residues: 251.7276 Evaluate side-chains 182 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 217 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10182 Z= 0.190 Angle : 0.546 7.714 13860 Z= 0.286 Chirality : 0.039 0.149 1644 Planarity : 0.002 0.021 1662 Dihedral : 4.080 28.877 1350 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.96 % Favored : 95.54 % Rotamer: Outliers : 1.98 % Allowed : 16.94 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.95 (0.24), residues: 1212 helix: 4.16 (0.14), residues: 876 sheet: 1.22 (0.50), residues: 60 loop : -2.80 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 132 HIS 0.002 0.001 HIS B 123 PHE 0.010 0.001 PHE E 31 TYR 0.006 0.001 TYR B 151 ARG 0.003 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.160 Fit side-chains REVERT: A 219 ARG cc_start: 0.2455 (OUTLIER) cc_final: 0.1261 (ttt180) REVERT: B 219 ARG cc_start: 0.2354 (OUTLIER) cc_final: 0.1204 (ttt180) REVERT: C 219 ARG cc_start: 0.2414 (OUTLIER) cc_final: 0.1300 (ttt180) REVERT: D 219 ARG cc_start: 0.2446 (OUTLIER) cc_final: 0.1252 (ttt180) REVERT: E 219 ARG cc_start: 0.2365 (OUTLIER) cc_final: 0.1188 (ttt180) REVERT: F 219 ARG cc_start: 0.2397 (OUTLIER) cc_final: 0.1273 (ttt180) outliers start: 22 outliers final: 8 residues processed: 178 average time/residue: 1.4047 time to fit residues: 266.6862 Evaluate side-chains 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10182 Z= 0.178 Angle : 0.529 6.838 13860 Z= 0.280 Chirality : 0.039 0.145 1644 Planarity : 0.002 0.014 1662 Dihedral : 3.925 27.223 1350 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.88 % Favored : 95.63 % Rotamer: Outliers : 2.25 % Allowed : 19.46 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.00 (0.24), residues: 1212 helix: 4.22 (0.15), residues: 876 sheet: 1.05 (0.52), residues: 60 loop : -2.83 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 132 HIS 0.001 0.000 HIS C 97 PHE 0.009 0.001 PHE E 31 TYR 0.009 0.001 TYR A 171 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.298 Fit side-chains REVERT: A 219 ARG cc_start: 0.2374 (OUTLIER) cc_final: 0.1235 (ttt180) REVERT: B 219 ARG cc_start: 0.2525 (OUTLIER) cc_final: 0.1345 (ttt180) REVERT: C 219 ARG cc_start: 0.2466 (OUTLIER) cc_final: 0.1350 (ttt180) REVERT: D 219 ARG cc_start: 0.2385 (OUTLIER) cc_final: 0.1243 (ttt180) REVERT: E 219 ARG cc_start: 0.2474 (OUTLIER) cc_final: 0.1286 (ttt180) REVERT: F 219 ARG cc_start: 0.2468 (OUTLIER) cc_final: 0.1337 (ttt180) outliers start: 25 outliers final: 11 residues processed: 176 average time/residue: 1.3227 time to fit residues: 248.2106 Evaluate side-chains 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10182 Z= 0.173 Angle : 0.537 6.482 13860 Z= 0.285 Chirality : 0.039 0.141 1644 Planarity : 0.002 0.012 1662 Dihedral : 3.811 25.658 1350 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.04 % Favored : 95.46 % Rotamer: Outliers : 2.52 % Allowed : 20.27 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.03 (0.24), residues: 1212 helix: 4.25 (0.15), residues: 876 sheet: 0.97 (0.52), residues: 60 loop : -2.81 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 132 HIS 0.003 0.001 HIS D 123 PHE 0.008 0.001 PHE B 31 TYR 0.006 0.001 TYR E 171 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.522 Fit side-chains REVERT: A 219 ARG cc_start: 0.2479 (OUTLIER) cc_final: 0.1349 (ttt180) REVERT: B 219 ARG cc_start: 0.2483 (OUTLIER) cc_final: 0.1363 (ttt180) REVERT: C 219 ARG cc_start: 0.2498 (OUTLIER) cc_final: 0.1374 (ttt180) REVERT: D 219 ARG cc_start: 0.2481 (OUTLIER) cc_final: 0.1350 (ttt180) REVERT: E 219 ARG cc_start: 0.2497 (OUTLIER) cc_final: 0.1347 (ttt180) REVERT: F 219 ARG cc_start: 0.2485 (OUTLIER) cc_final: 0.1387 (ttt180) outliers start: 28 outliers final: 7 residues processed: 175 average time/residue: 1.3407 time to fit residues: 250.1697 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10182 Z= 0.218 Angle : 0.569 7.263 13860 Z= 0.302 Chirality : 0.040 0.141 1644 Planarity : 0.003 0.019 1662 Dihedral : 3.949 25.729 1350 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.54 % Favored : 94.97 % Rotamer: Outliers : 2.43 % Allowed : 21.53 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.81 (0.24), residues: 1212 helix: 4.07 (0.15), residues: 876 sheet: 1.07 (0.53), residues: 60 loop : -2.87 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 132 HIS 0.004 0.001 HIS E 123 PHE 0.008 0.001 PHE E 180 TYR 0.008 0.001 TYR D 151 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.241 Fit side-chains REVERT: A 219 ARG cc_start: 0.2595 (OUTLIER) cc_final: 0.1439 (ttt180) REVERT: B 219 ARG cc_start: 0.2561 (OUTLIER) cc_final: 0.1409 (ttt180) REVERT: C 219 ARG cc_start: 0.2555 (OUTLIER) cc_final: 0.1412 (ttt180) REVERT: D 219 ARG cc_start: 0.2601 (OUTLIER) cc_final: 0.1441 (ttt180) REVERT: E 219 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.1427 (ttt180) REVERT: F 219 ARG cc_start: 0.2564 (OUTLIER) cc_final: 0.1410 (ttt180) outliers start: 27 outliers final: 11 residues processed: 163 average time/residue: 1.3180 time to fit residues: 228.6380 Evaluate side-chains 156 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10182 Z= 0.293 Angle : 0.623 8.580 13860 Z= 0.329 Chirality : 0.042 0.145 1644 Planarity : 0.003 0.029 1662 Dihedral : 4.190 26.210 1350 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.54 % Favored : 94.97 % Rotamer: Outliers : 1.89 % Allowed : 23.42 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.24), residues: 1212 helix: 3.96 (0.15), residues: 870 sheet: 1.61 (0.57), residues: 60 loop : -2.93 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 77 HIS 0.002 0.001 HIS B 123 PHE 0.009 0.002 PHE D 190 TYR 0.011 0.001 TYR B 151 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.220 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 158 average time/residue: 1.2620 time to fit residues: 213.5927 Evaluate side-chains 163 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 175 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10182 Z= 0.202 Angle : 0.597 7.664 13860 Z= 0.313 Chirality : 0.039 0.137 1644 Planarity : 0.003 0.016 1662 Dihedral : 3.951 25.427 1350 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.29 % Favored : 95.21 % Rotamer: Outliers : 2.43 % Allowed : 23.42 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.83 (0.24), residues: 1212 helix: 4.05 (0.15), residues: 876 sheet: 1.62 (0.62), residues: 60 loop : -2.87 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 132 HIS 0.001 0.000 HIS F 97 PHE 0.008 0.001 PHE C 31 TYR 0.008 0.001 TYR B 151 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.211 Fit side-chains REVERT: A 219 ARG cc_start: 0.2632 (OUTLIER) cc_final: 0.1465 (ttt180) REVERT: B 219 ARG cc_start: 0.2658 (OUTLIER) cc_final: 0.1523 (ttt180) REVERT: C 219 ARG cc_start: 0.2551 (OUTLIER) cc_final: 0.1409 (ttt180) REVERT: D 219 ARG cc_start: 0.2645 (OUTLIER) cc_final: 0.1471 (ttt180) REVERT: E 219 ARG cc_start: 0.2621 (OUTLIER) cc_final: 0.1473 (ttt180) REVERT: F 219 ARG cc_start: 0.2524 (OUTLIER) cc_final: 0.1362 (ttt180) outliers start: 27 outliers final: 15 residues processed: 164 average time/residue: 1.3539 time to fit residues: 236.2770 Evaluate side-chains 164 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN F 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10182 Z= 0.208 Angle : 0.614 8.666 13860 Z= 0.320 Chirality : 0.039 0.137 1644 Planarity : 0.002 0.019 1662 Dihedral : 3.931 24.920 1350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.70 % Favored : 94.80 % Rotamer: Outliers : 2.70 % Allowed : 22.70 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.82 (0.24), residues: 1212 helix: 4.01 (0.15), residues: 876 sheet: 1.71 (0.63), residues: 60 loop : -2.78 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 132 HIS 0.001 0.000 HIS C 97 PHE 0.008 0.001 PHE C 31 TYR 0.008 0.001 TYR B 151 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.177 Fit side-chains REVERT: A 219 ARG cc_start: 0.2629 (OUTLIER) cc_final: 0.1435 (ttt180) REVERT: B 219 ARG cc_start: 0.2637 (OUTLIER) cc_final: 0.1550 (ttt180) REVERT: C 219 ARG cc_start: 0.2425 (OUTLIER) cc_final: 0.1318 (ttt180) REVERT: D 219 ARG cc_start: 0.2630 (OUTLIER) cc_final: 0.1436 (ttt180) REVERT: E 219 ARG cc_start: 0.2659 (OUTLIER) cc_final: 0.1529 (ttt180) REVERT: F 219 ARG cc_start: 0.2428 (OUTLIER) cc_final: 0.1319 (ttt180) outliers start: 30 outliers final: 14 residues processed: 166 average time/residue: 1.3903 time to fit residues: 245.4781 Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0060 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN D 99 GLN F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10182 Z= 0.269 Angle : 0.654 8.965 13860 Z= 0.341 Chirality : 0.041 0.138 1644 Planarity : 0.003 0.022 1662 Dihedral : 4.083 25.427 1350 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.79 % Favored : 94.64 % Rotamer: Outliers : 2.34 % Allowed : 23.06 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.67 (0.24), residues: 1212 helix: 3.93 (0.15), residues: 870 sheet: 1.72 (0.62), residues: 60 loop : -2.80 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 132 HIS 0.002 0.001 HIS E 97 PHE 0.008 0.001 PHE E 190 TYR 0.010 0.001 TYR D 151 ARG 0.003 0.000 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.226 Fit side-chains REVERT: A 219 ARG cc_start: 0.2652 (OUTLIER) cc_final: 0.1445 (ttt180) REVERT: B 219 ARG cc_start: 0.2761 (OUTLIER) cc_final: 0.1639 (ttt180) REVERT: C 219 ARG cc_start: 0.2495 (OUTLIER) cc_final: 0.1377 (ttt180) REVERT: D 219 ARG cc_start: 0.2659 (OUTLIER) cc_final: 0.1453 (ttt180) REVERT: E 219 ARG cc_start: 0.2737 (OUTLIER) cc_final: 0.1581 (ttt180) REVERT: F 219 ARG cc_start: 0.2491 (OUTLIER) cc_final: 0.1377 (ttt180) outliers start: 26 outliers final: 15 residues processed: 161 average time/residue: 1.3664 time to fit residues: 234.2185 Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 219 ARG Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 219 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN D 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068406 restraints weight = 19536.780| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.40 r_work: 0.2830 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10182 Z= 0.222 Angle : 0.657 9.914 13860 Z= 0.343 Chirality : 0.040 0.151 1644 Planarity : 0.003 0.028 1662 Dihedral : 3.998 25.191 1350 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.70 % Favored : 94.64 % Rotamer: Outliers : 2.07 % Allowed : 22.97 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.79 (0.24), residues: 1212 helix: 3.96 (0.15), residues: 876 sheet: 1.65 (0.61), residues: 60 loop : -2.69 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 132 HIS 0.001 0.000 HIS C 94 PHE 0.008 0.001 PHE C 31 TYR 0.010 0.001 TYR B 211 ARG 0.005 0.000 ARG E 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.16 seconds wall clock time: 71 minutes 51.22 seconds (4311.22 seconds total)