Starting phenix.real_space_refine on Sun Mar 10 17:11:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot4_17168/03_2024/8ot4_17168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot4_17168/03_2024/8ot4_17168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot4_17168/03_2024/8ot4_17168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot4_17168/03_2024/8ot4_17168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot4_17168/03_2024/8ot4_17168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ot4_17168/03_2024/8ot4_17168.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 12 5.16 5 C 2184 2.51 5 N 600 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "F PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 5": "NH1" <-> "NH2" Residue "H TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "K PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 5": "NH1" <-> "NH2" Residue "K TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 22": "OE1" <-> "OE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 5": "NH1" <-> "NH2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 22": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "C" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "I" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "J" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "K" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "L" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 287 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Time building chain proxies: 2.16, per 1000 atoms: 0.63 Number of scatterers: 3444 At special positions: 0 Unit cell: (75.92, 80.08, 49.92, 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 12 16.00 O 648 8.00 N 600 7.00 C 2184 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: 1.12 Conformation dependent library (CDL) restraints added in 589.8 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.588A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 11 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU I 11 " --> pdb=" O VAL K 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 24 removed outlier: 6.562A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA K 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE I 20 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP K 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU I 22 " --> pdb=" O ASP K 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.589A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU J 11 " --> pdb=" O VAL L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 24 removed outlier: 6.563A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA L 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE J 20 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP L 23 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU J 22 " --> pdb=" O ASP L 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 No hydrogen bonds 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: 0.09 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 800 1.33 - 1.45: 808 1.45 - 1.56: 1884 1.56 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 3516 Sorted by residual: bond pdb=" N VAL K 36 " pdb=" CA VAL K 36 " ideal model delta sigma weight residual 1.459 1.493 -0.035 1.19e-02 7.06e+03 8.42e+00 bond pdb=" N VAL G 36 " pdb=" CA VAL G 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.31e+00 bond pdb=" N VAL I 36 " pdb=" CA VAL I 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N VAL J 36 " pdb=" CA VAL J 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.21e+00 bond pdb=" N VAL D 36 " pdb=" CA VAL D 36 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.20e+00 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 100.28 - 106.75: 276 106.75 - 113.22: 1344 113.22 - 119.70: 1620 119.70 - 126.17: 1416 126.17 - 132.64: 48 Bond angle restraints: 4704 Sorted by residual: angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 112.04 101.75 10.29 1.44e+00 4.82e-01 5.10e+01 angle pdb=" N GLU L 22 " pdb=" CA GLU L 22 " pdb=" C GLU L 22 " ideal model delta sigma weight residual 112.04 101.77 10.27 1.44e+00 4.82e-01 5.09e+01 angle pdb=" N GLU J 22 " pdb=" CA GLU J 22 " pdb=" C GLU J 22 " ideal model delta sigma weight residual 112.04 101.77 10.27 1.44e+00 4.82e-01 5.09e+01 angle pdb=" N GLU B 22 " pdb=" CA GLU B 22 " pdb=" C GLU B 22 " ideal model delta sigma weight residual 112.04 101.78 10.26 1.44e+00 4.82e-01 5.08e+01 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 112.04 101.78 10.26 1.44e+00 4.82e-01 5.08e+01 ... (remaining 4699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.93: 1560 10.93 - 21.86: 240 21.86 - 32.78: 132 32.78 - 43.71: 12 43.71 - 54.64: 36 Dihedral angle restraints: 1980 sinusoidal: 768 harmonic: 1212 Sorted by residual: dihedral pdb=" CA ILE E 31 " pdb=" CB ILE E 31 " pdb=" CG1 ILE E 31 " pdb=" CD1 ILE E 31 " ideal model delta sinusoidal sigma weight residual 60.00 109.27 -49.27 3 1.50e+01 4.44e-03 8.75e+00 dihedral pdb=" CA ILE C 31 " pdb=" CB ILE C 31 " pdb=" CG1 ILE C 31 " pdb=" CD1 ILE C 31 " ideal model delta sinusoidal sigma weight residual 60.00 109.27 -49.27 3 1.50e+01 4.44e-03 8.75e+00 dihedral pdb=" CA ILE F 31 " pdb=" CB ILE F 31 " pdb=" CG1 ILE F 31 " pdb=" CD1 ILE F 31 " ideal model delta sinusoidal sigma weight residual 60.00 109.26 -49.26 3 1.50e+01 4.44e-03 8.75e+00 ... (remaining 1977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 74 0.056 - 0.112: 186 0.112 - 0.168: 135 0.168 - 0.224: 73 0.224 - 0.280: 12 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA ILE G 31 " pdb=" N ILE G 31 " pdb=" C ILE G 31 " pdb=" CB ILE G 31 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 477 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 31 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ILE I 31 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE I 31 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE I 32 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 31 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ILE K 31 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE K 31 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE K 32 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 31 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ILE E 31 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE E 31 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE E 32 " -0.024 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 1668 3.00 - 3.48: 3051 3.48 - 3.95: 5775 3.95 - 4.43: 6610 4.43 - 4.90: 12473 Nonbonded interactions: 29577 Sorted by model distance: nonbonded pdb=" N HIS E 13 " pdb=" O HIS E 13 " model vdw 2.527 2.496 nonbonded pdb=" N HIS I 13 " pdb=" O HIS I 13 " model vdw 2.528 2.496 nonbonded pdb=" N HIS C 13 " pdb=" O HIS C 13 " model vdw 2.528 2.496 nonbonded pdb=" N HIS F 13 " pdb=" O HIS F 13 " model vdw 2.528 2.496 nonbonded pdb=" N HIS H 13 " pdb=" O HIS H 13 " model vdw 2.528 2.496 ... (remaining 29572 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.370 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: 1.800 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.012 0.036 3516 Z= 0.892 Angle : 2.301 10.287 4704 Z= 1.670 Chirality : 0.127 0.280 480 Planarity : 0.014 0.039 624 Dihedral : 15.194 54.635 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 6 PHE 0.012 0.003 PHE I 4 TYR 0.005 0.002 TYR C 10 ARG 0.002 0.001 ARG K 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 TYR cc_start: 0.7942 (t80) cc_final: 0.5769 (p90) REVERT: L 5 ARG cc_start: 0.7697 (mtp180) cc_final: 0.6683 (tpt170) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 1.2090 time to fit residues: 161.3402 Evaluate side-chains 108 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 5.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN G 6 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 HIS ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3516 Z= 0.132 Angle : 0.621 4.916 4704 Z= 0.329 Chirality : 0.049 0.124 480 Planarity : 0.002 0.011 624 Dihedral : 5.566 16.712 456 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.01 % Allowed : 25.57 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 13 PHE 0.014 0.003 PHE G 20 TYR 0.011 0.001 TYR I 10 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: C 3 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: C 28 LYS cc_start: 0.8050 (tttt) cc_final: 0.7799 (ttpt) REVERT: F 3 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: F 11 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6860 (tt0) REVERT: G 3 GLU cc_start: 0.7418 (tt0) cc_final: 0.7094 (tm-30) REVERT: I 28 LYS cc_start: 0.7964 (tmtp) cc_final: 0.7737 (ttmt) REVERT: J 28 LYS cc_start: 0.8102 (tmmm) cc_final: 0.7769 (ttpt) outliers start: 7 outliers final: 0 residues processed: 94 average time/residue: 1.3009 time to fit residues: 125.4649 Evaluate side-chains 85 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain F residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 3516 Z= 0.297 Angle : 0.744 5.239 4704 Z= 0.403 Chirality : 0.051 0.127 480 Planarity : 0.003 0.012 624 Dihedral : 6.158 20.840 456 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 3.74 % Allowed : 24.71 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.34), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 13 PHE 0.025 0.004 PHE A 4 TYR 0.007 0.001 TYR G 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.5430 (tppt) REVERT: C 3 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: C 11 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6720 (tt0) REVERT: D 11 GLU cc_start: 0.7516 (tt0) cc_final: 0.7000 (tt0) REVERT: G 11 GLU cc_start: 0.7183 (tt0) cc_final: 0.6844 (tt0) REVERT: I 28 LYS cc_start: 0.8095 (tmtp) cc_final: 0.7877 (ttmt) REVERT: J 28 LYS cc_start: 0.8244 (tmmm) cc_final: 0.7984 (ttpt) REVERT: L 5 ARG cc_start: 0.7863 (mtp180) cc_final: 0.6795 (tpt170) outliers start: 13 outliers final: 2 residues processed: 89 average time/residue: 1.4812 time to fit residues: 134.8298 Evaluate side-chains 87 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain F residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3516 Z= 0.133 Angle : 0.592 4.080 4704 Z= 0.316 Chirality : 0.050 0.123 480 Planarity : 0.002 0.010 624 Dihedral : 5.504 19.843 456 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.75 % Allowed : 25.29 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 13 PHE 0.011 0.002 PHE J 4 TYR 0.004 0.000 TYR K 10 ARG 0.001 0.000 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.369 Fit side-chains REVERT: B 3 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: B 5 ARG cc_start: 0.7937 (mtp180) cc_final: 0.6833 (ttp-170) REVERT: C 3 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: C 5 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7656 (mtp180) REVERT: F 3 GLU cc_start: 0.7490 (tt0) cc_final: 0.6765 (tm-30) REVERT: G 3 GLU cc_start: 0.7378 (tt0) cc_final: 0.6910 (tm-30) REVERT: I 28 LYS cc_start: 0.8127 (tmtp) cc_final: 0.7785 (ttpt) REVERT: J 3 GLU cc_start: 0.7441 (tt0) cc_final: 0.7017 (tm-30) REVERT: J 28 LYS cc_start: 0.8180 (tmmm) cc_final: 0.7864 (ttpt) REVERT: L 5 ARG cc_start: 0.7794 (mtp180) cc_final: 0.6683 (tpt170) outliers start: 20 outliers final: 3 residues processed: 93 average time/residue: 1.4361 time to fit residues: 136.6809 Evaluate side-chains 82 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3516 Z= 0.179 Angle : 0.613 4.256 4704 Z= 0.332 Chirality : 0.050 0.127 480 Planarity : 0.002 0.010 624 Dihedral : 5.522 20.055 456 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.16 % Allowed : 27.87 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS G 13 PHE 0.015 0.003 PHE E 4 TYR 0.004 0.001 TYR D 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.368 Fit side-chains REVERT: B 3 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: B 5 ARG cc_start: 0.7951 (mtp180) cc_final: 0.6820 (ttp-170) REVERT: C 3 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: C 5 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7626 (mtp180) REVERT: G 3 GLU cc_start: 0.7331 (tt0) cc_final: 0.6868 (tm-30) REVERT: G 5 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7545 (ttp80) REVERT: I 28 LYS cc_start: 0.8159 (tmtp) cc_final: 0.7872 (ttmt) REVERT: J 28 LYS cc_start: 0.8181 (tmmm) cc_final: 0.7898 (ttpt) REVERT: L 5 ARG cc_start: 0.7798 (mtp180) cc_final: 0.6683 (tpt170) outliers start: 11 outliers final: 5 residues processed: 86 average time/residue: 1.5025 time to fit residues: 132.1477 Evaluate side-chains 87 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3516 Z= 0.110 Angle : 0.554 4.277 4704 Z= 0.295 Chirality : 0.050 0.129 480 Planarity : 0.002 0.008 624 Dihedral : 5.088 16.422 456 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.74 % Allowed : 28.16 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 13 PHE 0.008 0.002 PHE E 4 TYR 0.005 0.000 TYR D 10 ARG 0.000 0.000 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.442 Fit side-chains REVERT: A 11 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6921 (tt0) REVERT: B 3 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: B 5 ARG cc_start: 0.7968 (mtp180) cc_final: 0.6835 (ttp-170) REVERT: C 3 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: C 5 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7612 (mtp180) REVERT: D 15 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: F 3 GLU cc_start: 0.7396 (tt0) cc_final: 0.6749 (tm-30) REVERT: G 3 GLU cc_start: 0.7310 (tt0) cc_final: 0.6937 (tm-30) REVERT: G 5 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7480 (tpp80) REVERT: J 3 GLU cc_start: 0.7471 (tt0) cc_final: 0.6905 (tm-30) REVERT: J 28 LYS cc_start: 0.8046 (tmmm) cc_final: 0.7747 (ttpt) REVERT: L 5 ARG cc_start: 0.7804 (mtp180) cc_final: 0.6743 (tpt170) outliers start: 13 outliers final: 5 residues processed: 90 average time/residue: 1.4826 time to fit residues: 136.4678 Evaluate side-chains 84 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain D residue 15 GLN Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3516 Z= 0.192 Angle : 0.629 4.558 4704 Z= 0.343 Chirality : 0.050 0.127 480 Planarity : 0.002 0.016 624 Dihedral : 5.472 17.137 456 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.60 % Allowed : 29.02 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 13 PHE 0.016 0.003 PHE I 4 TYR 0.004 0.000 TYR F 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.407 Fit side-chains REVERT: A 11 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6962 (tt0) REVERT: A 28 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.5300 (tppt) REVERT: B 3 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: C 3 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: C 5 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7628 (mtp180) REVERT: F 3 GLU cc_start: 0.7435 (tt0) cc_final: 0.6764 (tm-30) REVERT: G 3 GLU cc_start: 0.7338 (tt0) cc_final: 0.6891 (tm-30) REVERT: G 28 LYS cc_start: 0.8131 (tmmm) cc_final: 0.7883 (ttmt) REVERT: J 3 GLU cc_start: 0.7495 (tt0) cc_final: 0.6800 (tm-30) REVERT: J 28 LYS cc_start: 0.8159 (tmmm) cc_final: 0.7882 (ttpt) REVERT: L 5 ARG cc_start: 0.7812 (mtp180) cc_final: 0.6845 (tpt170) outliers start: 16 outliers final: 6 residues processed: 78 average time/residue: 1.5311 time to fit residues: 122.2040 Evaluate side-chains 83 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3516 Z= 0.302 Angle : 0.729 5.422 4704 Z= 0.400 Chirality : 0.051 0.129 480 Planarity : 0.003 0.011 624 Dihedral : 6.093 19.732 456 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.89 % Allowed : 29.60 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.024 0.004 PHE I 4 TYR 0.012 0.001 TYR K 10 ARG 0.002 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.370 Fit side-chains REVERT: A 28 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5008 (tppt) REVERT: B 5 ARG cc_start: 0.7955 (mtp180) cc_final: 0.6851 (ttp-170) REVERT: B 11 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7087 (tp30) REVERT: B 13 HIS cc_start: 0.4918 (m-70) cc_final: 0.4610 (t-90) REVERT: C 3 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: F 3 GLU cc_start: 0.7378 (tt0) cc_final: 0.6687 (tm-30) REVERT: G 28 LYS cc_start: 0.8209 (tmmm) cc_final: 0.7917 (ttpt) REVERT: J 28 LYS cc_start: 0.8232 (tmmm) cc_final: 0.7924 (ttpt) REVERT: K 5 ARG cc_start: 0.7677 (mtp180) cc_final: 0.6542 (tpt170) REVERT: L 5 ARG cc_start: 0.7810 (mtp180) cc_final: 0.6795 (tpt170) outliers start: 17 outliers final: 7 residues processed: 86 average time/residue: 1.5500 time to fit residues: 136.2356 Evaluate side-chains 87 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3516 Z= 0.145 Angle : 0.615 5.208 4704 Z= 0.331 Chirality : 0.050 0.125 480 Planarity : 0.002 0.016 624 Dihedral : 5.629 18.874 456 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.16 % Allowed : 32.47 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 13 PHE 0.013 0.002 PHE I 4 TYR 0.003 0.000 TYR J 10 ARG 0.002 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.419 Fit side-chains REVERT: B 3 GLU cc_start: 0.7517 (tt0) cc_final: 0.7130 (tm-30) REVERT: B 5 ARG cc_start: 0.7944 (mtp180) cc_final: 0.6588 (ptt-90) REVERT: C 1 ASP cc_start: 0.6997 (p0) cc_final: 0.6443 (m-30) REVERT: C 3 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: C 5 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7654 (mtp180) REVERT: F 3 GLU cc_start: 0.7382 (tt0) cc_final: 0.6736 (tm-30) REVERT: G 3 GLU cc_start: 0.7243 (tt0) cc_final: 0.6825 (tm-30) REVERT: G 28 LYS cc_start: 0.8119 (tmmm) cc_final: 0.7879 (ttmt) REVERT: I 3 GLU cc_start: 0.7434 (tt0) cc_final: 0.7000 (tm-30) REVERT: J 28 LYS cc_start: 0.8183 (tmmm) cc_final: 0.7860 (ttpt) REVERT: L 5 ARG cc_start: 0.7838 (mtp180) cc_final: 0.6745 (tpt170) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 1.5347 time to fit residues: 122.4726 Evaluate side-chains 81 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3516 Z= 0.261 Angle : 0.706 6.039 4704 Z= 0.385 Chirality : 0.051 0.128 480 Planarity : 0.002 0.020 624 Dihedral : 5.999 21.077 456 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 32.76 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.35), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.020 0.003 PHE I 4 TYR 0.012 0.001 TYR K 10 ARG 0.006 0.000 ARG J 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.422 Fit side-chains REVERT: B 3 GLU cc_start: 0.7573 (tt0) cc_final: 0.7095 (tm-30) REVERT: B 5 ARG cc_start: 0.7936 (mtp180) cc_final: 0.6842 (ttp-170) REVERT: B 11 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6876 (tp30) REVERT: C 3 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: D 5 ARG cc_start: 0.7831 (mtp180) cc_final: 0.7616 (tpp80) REVERT: F 3 GLU cc_start: 0.7409 (tt0) cc_final: 0.6660 (tm-30) REVERT: G 28 LYS cc_start: 0.8141 (tmmm) cc_final: 0.7835 (ttpt) REVERT: I 3 GLU cc_start: 0.7421 (tt0) cc_final: 0.6877 (tm-30) REVERT: J 28 LYS cc_start: 0.8271 (tmmm) cc_final: 0.7916 (ttpt) REVERT: K 5 ARG cc_start: 0.7691 (mtp180) cc_final: 0.6532 (tpt170) REVERT: L 5 ARG cc_start: 0.7829 (mtp180) cc_final: 0.6817 (tpt170) outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 1.6385 time to fit residues: 132.2030 Evaluate side-chains 81 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain K residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.124279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.103337 restraints weight = 5230.548| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 3.10 r_work: 0.3890 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3516 Z= 0.215 Angle : 0.672 5.980 4704 Z= 0.366 Chirality : 0.051 0.128 480 Planarity : 0.002 0.012 624 Dihedral : 5.927 19.284 456 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.30 % Allowed : 33.33 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.36), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.017 0.003 PHE I 4 TYR 0.004 0.001 TYR F 10 ARG 0.001 0.000 ARG F 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.19 seconds wall clock time: 43 minutes 14.58 seconds (2594.58 seconds total)