Starting phenix.real_space_refine on Sat Apr 26 23:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb2_61305/04_2025/9jb2_61305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb2_61305/04_2025/9jb2_61305.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/cci-nas-00/data/ceres_data/9jb2_61305/04_2025/9jb2_61305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb2_61305/04_2025/9jb2_61305.map" model { file = "/net/cci-nas-00/data/ceres_data/9jb2_61305/04_2025/9jb2_61305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb2_61305/04_2025/9jb2_61305.cif" } 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 15 5.16 5 C 2520 2.51 5 N 650 2.21 5 O 705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3890 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 130 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Conformer: "B" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} bond proxies already assigned to first conformer: 114 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "A" Number of atoms: 130 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Conformer: "B" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} bond proxies already assigned to first conformer: 114 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 130 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Conformer: "B" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} bond proxies already assigned to first conformer: 114 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 130 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Conformer: "B" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} bond proxies already assigned to first conformer: 114 Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "E" Number of atoms: 130 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Conformer: "B" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} bond proxies already assigned to first conformer: 114 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "CC" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CC" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 135 Classifications: {'peptide': 16} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 15} Chain: "CC" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "BE" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "BE" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "BD" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "BD" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "BC" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "BC" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "BB" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "BB" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "BA" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "BA" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "CB" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CB" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 135 Classifications: {'peptide': 16} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 15} Chain: "CB" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "CA" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CA" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 135 Classifications: {'peptide': 16} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 15} Chain: "CA" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "CD" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CD" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 135 Classifications: {'peptide': 16} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 15} Chain: "CD" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Chain: "CE" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "CE" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 135 Classifications: {'peptide': 16} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 15} Chain: "CE" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Time building chain proxies: 3.36, per 1000 atoms: 0.86 Number of scatterers: 3890 At special positions: 0 Unit cell: (91.3, 73.04, 42.33, 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 15 16.00 O 705 8.00 N 650 7.00 C 2520 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 - 3.00 Amino acid : True - 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 Links applied TRANS " DAS A 23 " - " GLU A 22 " " DAS B 23 " - " GLU B 22 " " DAS C 23 " - " GLU C 22 " " DAS D 23 " - " GLU D 22 " " DAS E 23 " - " GLU E 22 " " DASBA 23 " - " GLUBA 22 " " DASBB 23 " - " GLUBB 22 " " DASBC 23 " - " GLUBC 22 " " DASBD 23 " - " GLUBD 22 " " DASBE 23 " - " GLUBE 22 " " DASCA 7 " - " HISCA 6 " " DASCA 23 " - " GLUCA 22 " " DASCB 7 " - " HISCB 6 " " DASCB 23 " - " GLUCB 22 " " DASCC 7 " - " HISCC 6 " " DASCC 23 " - " GLUCC 22 " " DASCD 7 " - " HISCD 6 " " DASCD 23 " - " GLUCD 22 " " DASCE 7 " - " HISCE 6 " " DASCE 23 " - " GLUCE 22 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 496.3 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAS C 23 " pdb=" CB DAS A 23 " pdb=" CB DAS B 23 " pdb=" CB DAS D 23 " pdb=" CB DAS E 23 " pdb=" CB DASCC 7 " pdb=" CB DASCC 23 " pdb=" CB DASBE 23 " pdb=" CB DASBD 23 " pdb=" CB DASBC 23 " pdb=" CB DASBB 23 " pdb=" CB DASBA 23 " pdb=" CB DASCB 7 " pdb=" CB DASCB 23 " pdb=" CB DASCA 7 " pdb=" CB DASCA 23 " pdb=" CB DASCD 7 " pdb=" CB DASCD 23 " pdb=" CB DASCE 7 " pdb=" CB DASCE 23 " Number of C-beta restraints generated: 840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... 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: 0.00 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1260 1.34 - 1.45: 537 1.45 - 1.57: 2108 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 3935 Sorted by residual: bond pdb=" C VALBE 24 " pdb=" N GLYBE 25 " ideal model delta sigma weight residual 1.332 1.336 -0.004 5.00e-03 4.00e+04 5.84e-01 bond pdb=" CB APHE D 19 " pdb=" CG APHE D 19 " ideal model delta sigma weight residual 1.502 1.485 0.017 2.30e-02 1.89e+03 5.73e-01 bond pdb=" CB APHE B 19 " pdb=" CG APHE B 19 " ideal model delta sigma weight residual 1.502 1.485 0.017 2.30e-02 1.89e+03 5.56e-01 bond pdb=" CA ALA E 21 " pdb=" CB ALA E 21 " ideal model delta sigma weight residual 1.531 1.507 0.024 3.28e-02 9.30e+02 5.34e-01 bond pdb=" CA ALA D 21 " pdb=" CB ALA D 21 " ideal model delta sigma weight residual 1.531 1.508 0.023 3.28e-02 9.30e+02 4.98e-01 ... (remaining 3930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.70: 4803 0.70 - 1.40: 393 1.40 - 2.09: 40 2.09 - 2.79: 23 2.79 - 3.49: 6 Bond angle restraints: 5265 Sorted by residual: angle pdb=" O GLYCD 9 " pdb=" C GLYCD 9 " pdb=" N TYRCD 10 " ideal model delta sigma weight residual 123.35 122.58 0.77 6.30e-01 2.52e+00 1.49e+00 angle pdb=" O GLYCE 9 " pdb=" C GLYCE 9 " pdb=" N TYRCE 10 " ideal model delta sigma weight residual 123.35 122.63 0.72 6.30e-01 2.52e+00 1.32e+00 angle pdb=" C HISCD 13 " pdb=" N HISCD 14 " pdb=" CA HISCD 14 " ideal model delta sigma weight residual 122.36 123.99 -1.63 1.42e+00 4.96e-01 1.31e+00 angle pdb=" CA GLYCD 9 " pdb=" C GLYCD 9 " pdb=" N TYRCD 10 " ideal model delta sigma weight residual 115.82 117.04 -1.22 1.10e+00 8.26e-01 1.23e+00 angle pdb=" N HISCC 13 " pdb=" CA HISCC 13 " pdb=" C HISCC 13 " ideal model delta sigma weight residual 108.60 110.21 -1.61 1.46e+00 4.69e-01 1.22e+00 ... (remaining 5260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2062 17.73 - 35.45: 108 35.45 - 53.18: 28 53.18 - 70.91: 16 70.91 - 88.64: 16 Dihedral angle restraints: 2230 sinusoidal: 865 harmonic: 1365 Sorted by residual: dihedral pdb=" CA GLUCA 3 " pdb=" CB GLUCA 3 " pdb=" CG GLUCA 3 " pdb=" CD GLUCA 3 " ideal model delta sinusoidal sigma weight residual 60.00 119.63 -59.63 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLUCD 3 " pdb=" CB GLUCD 3 " pdb=" CG GLUCD 3 " pdb=" CD GLUCD 3 " ideal model delta sinusoidal sigma weight residual 180.00 121.78 58.22 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLUCB 3 " pdb=" CB GLUCB 3 " pdb=" CG GLUCB 3 " pdb=" CD GLUCB 3 " ideal model delta sinusoidal sigma weight residual 180.00 121.97 58.03 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 285 0.028 - 0.056: 158 0.056 - 0.084: 56 0.084 - 0.112: 77 0.112 - 0.140: 24 Chirality restraints: 600 Sorted by residual: chirality pdb=" CA ILECD 31 " pdb=" N ILECD 31 " pdb=" C ILECD 31 " pdb=" CB ILECD 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILECE 31 " pdb=" N ILECE 31 " pdb=" C ILECE 31 " pdb=" CB ILECE 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILECB 31 " pdb=" N ILECB 31 " pdb=" C ILECB 31 " pdb=" CB ILECB 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 597 not shown) Planarity restraints: 695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BPHE E 19 " -0.007 2.00e-02 2.50e+03 6.30e-03 6.96e-01 pdb=" CG BPHE E 19 " 0.015 2.00e-02 2.50e+03 pdb=" CD1BPHE E 19 " -0.003 2.00e-02 2.50e+03 pdb=" CD2BPHE E 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE1BPHE E 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2BPHE E 19 " -0.002 2.00e-02 2.50e+03 pdb=" CZ BPHE E 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BPHE C 19 " -0.006 2.00e-02 2.50e+03 5.61e-03 5.51e-01 pdb=" CG BPHE C 19 " 0.013 2.00e-02 2.50e+03 pdb=" CD1BPHE C 19 " -0.003 2.00e-02 2.50e+03 pdb=" CD2BPHE C 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE1BPHE C 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2BPHE C 19 " -0.002 2.00e-02 2.50e+03 pdb=" CZ BPHE C 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BPHE D 19 " -0.006 2.00e-02 2.50e+03 5.19e-03 4.71e-01 pdb=" CG BPHE D 19 " 0.012 2.00e-02 2.50e+03 pdb=" CD1BPHE D 19 " -0.002 2.00e-02 2.50e+03 pdb=" CD2BPHE D 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE1BPHE D 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2BPHE D 19 " -0.002 2.00e-02 2.50e+03 pdb=" CZ BPHE D 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 692 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 679 2.79 - 3.31: 3264 3.31 - 3.84: 6678 3.84 - 4.37: 7533 4.37 - 4.90: 14480 Nonbonded interactions: 32634 Sorted by model distance: nonbonded pdb=" NZ LYS A 16 " pdb=" OXT ALACA 42 " model vdw 2.256 3.120 nonbonded pdb=" NZ LYS B 16 " pdb=" OXT ALACB 42 " model vdw 2.263 3.120 nonbonded pdb=" OXT ALA D 42 " pdb=" NZ LYSBD 28 " model vdw 2.270 3.120 nonbonded pdb=" OXT ALA C 42 " pdb=" NZ LYSBC 28 " model vdw 2.286 3.120 nonbonded pdb=" OXT ALA E 42 " pdb=" NZ LYSBE 28 " model vdw 2.330 3.120 ... (remaining 32629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 18 or resid 20 through 22 or resid 23 through 42 \ )) selection = (chain 'B' and (resid 9 through 18 or resid 20 through 22 or resid 23 through 42 \ )) selection = (chain 'C' and (resid 9 through 18 or resid 20 through 22 or resid 23 through 42 \ )) selection = (chain 'D' and (resid 9 through 18 or resid 20 through 22 or resid 23 through 42 \ )) selection = (chain 'E' and (resid 9 through 18 or resid 20 through 22 or resid 23 through 42 \ )) } ncs_group { reference = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' } ncs_group { reference = chain 'CA' selection = chain 'CB' selection = chain 'CC' selection = chain 'CD' selection = chain 'CE' } 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=0.39 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 0.028 3955 Z= 0.158 Angle : 0.429 3.488 5325 Z= 0.230 Chirality : 0.054 0.140 600 Planarity : 0.002 0.007 675 Dihedral : 12.568 81.988 1330 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.27 % Allowed : 4.86 % Favored : 94.86 % 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: -2.12 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCA 14 PHE 0.010 0.001 PHE D 20 TYR 0.008 0.001 TYRCB 10 ARG 0.001 0.000 ARGCA 5 Details of bonding type rmsd link_TRANS : bond 0.00143 ( 20) link_TRANS : angle 0.40643 ( 60) covalent geometry : bond 0.00351 ( 3935) covalent geometry : angle 0.42923 ( 5265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.406 Fit side-chains REVERT: C 11 GLU cc_start: 0.7898 (tt0) cc_final: 0.7583 (tt0) REVERT: A 11 GLU cc_start: 0.7957 (tt0) cc_final: 0.7713 (tt0) REVERT: B 11 GLU cc_start: 0.8197 (tt0) cc_final: 0.7972 (tt0) REVERT: E 11 GLU cc_start: 0.8045 (tt0) cc_final: 0.7791 (tt0) REVERT: E 34 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8494 (tt) REVERT: BE 35 MET cc_start: 0.8639 (tpt) cc_final: 0.8270 (tpt) REVERT: BD 15 GLN cc_start: 0.5776 (mt0) cc_final: 0.5344 (mt0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 1.1082 time to fit residues: 98.5815 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS B 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.129094 restraints weight = 16307.566| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 8.19 r_work: 0.3441 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3955 Z= 0.138 Angle : 0.413 5.104 5325 Z= 0.217 Chirality : 0.054 0.138 600 Planarity : 0.002 0.007 675 Dihedral : 9.842 73.545 567 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.24 % Allowed : 10.27 % Favored : 86.49 % 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: -2.10 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCB 6 PHE 0.016 0.001 PHEBB 19 TYR 0.007 0.001 TYRCB 10 ARG 0.001 0.000 ARGCA 5 Details of bonding type rmsd link_TRANS : bond 0.00140 ( 20) link_TRANS : angle 0.40215 ( 60) covalent geometry : bond 0.00317 ( 3935) covalent geometry : angle 0.41349 ( 5265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.407 Fit side-chains REVERT: C 11 GLU cc_start: 0.7898 (tt0) cc_final: 0.7608 (tt0) REVERT: A 11 GLU cc_start: 0.7920 (tt0) cc_final: 0.7639 (tt0) REVERT: A 34 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 11 GLU cc_start: 0.8261 (tt0) cc_final: 0.7980 (tt0) REVERT: E 11 GLU cc_start: 0.8142 (tt0) cc_final: 0.7879 (tt0) REVERT: BE 35 MET cc_start: 0.8316 (tpt) cc_final: 0.7918 (tpt) REVERT: BD 15 GLN cc_start: 0.4901 (mt0) cc_final: 0.4692 (mt0) REVERT: BB 35 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8559 (tpt) outliers start: 12 outliers final: 1 residues processed: 79 average time/residue: 1.0162 time to fit residues: 83.3929 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.0060 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 22 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.181664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.133370 restraints weight = 14220.717| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 7.91 r_work: 0.3521 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3955 Z= 0.096 Angle : 0.376 5.629 5325 Z= 0.197 Chirality : 0.054 0.135 600 Planarity : 0.001 0.006 675 Dihedral : 10.316 79.697 565 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.78 % Allowed : 11.89 % Favored : 84.32 % 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: -2.03 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCB 6 PHE 0.010 0.001 PHEBE 19 TYR 0.008 0.001 TYR C 10 ARG 0.000 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00086 ( 20) link_TRANS : angle 0.33628 ( 60) covalent geometry : bond 0.00215 ( 3935) covalent geometry : angle 0.37674 ( 5265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.351 Fit side-chains REVERT: C 11 GLU cc_start: 0.7893 (tt0) cc_final: 0.7610 (tt0) REVERT: C 34 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 11 GLU cc_start: 0.7958 (tt0) cc_final: 0.7679 (tt0) REVERT: A 34 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8482 (tt) REVERT: B 11 GLU cc_start: 0.8259 (tt0) cc_final: 0.8056 (tt0) REVERT: D 34 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8513 (tt) REVERT: E 11 GLU cc_start: 0.8124 (tt0) cc_final: 0.7885 (tt0) REVERT: E 34 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8601 (tt) REVERT: BE 35 MET cc_start: 0.8105 (tpt) cc_final: 0.7683 (mmm) REVERT: BC 35 MET cc_start: 0.8518 (tpt) cc_final: 0.7773 (ttt) REVERT: BB 35 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8430 (tpt) REVERT: CE 3 GLU cc_start: 0.7576 (tt0) cc_final: 0.6652 (tt0) outliers start: 14 outliers final: 3 residues processed: 82 average time/residue: 0.8833 time to fit residues: 75.6327 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.173647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.126531 restraints weight = 15444.533| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 8.52 r_work: 0.3373 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3955 Z= 0.345 Angle : 0.626 5.211 5325 Z= 0.325 Chirality : 0.058 0.156 600 Planarity : 0.003 0.017 675 Dihedral : 11.828 88.632 565 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.24 % Allowed : 14.59 % Favored : 82.16 % 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: -2.43 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HISCC 6 PHE 0.024 0.003 PHE E 20 TYR 0.024 0.003 TYR C 10 ARG 0.003 0.001 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00355 ( 20) link_TRANS : angle 0.69406 ( 60) covalent geometry : bond 0.00795 ( 3935) covalent geometry : angle 0.62498 ( 5265) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.414 Fit side-chains REVERT: C 11 GLU cc_start: 0.7973 (tt0) cc_final: 0.7696 (tt0) REVERT: C 34 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 11 GLU cc_start: 0.7941 (tt0) cc_final: 0.7703 (tt0) REVERT: A 34 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 11 GLU cc_start: 0.8308 (tt0) cc_final: 0.8095 (tt0) REVERT: D 34 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8454 (tt) REVERT: E 11 GLU cc_start: 0.8003 (tt0) cc_final: 0.7800 (tt0) REVERT: CC 26 SER cc_start: 0.8148 (m) cc_final: 0.7681 (t) REVERT: BC 35 MET cc_start: 0.8439 (tpt) cc_final: 0.7651 (ttt) REVERT: BB 35 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8413 (tpt) REVERT: BA 36 VAL cc_start: 0.8538 (t) cc_final: 0.8173 (m) REVERT: CB 35 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7936 (tmm) REVERT: CA 8 SER cc_start: 0.8579 (p) cc_final: 0.8275 (p) REVERT: CE 8 SER cc_start: 0.8518 (p) cc_final: 0.8234 (m) outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 0.8435 time to fit residues: 71.3922 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain BE residue 18 VAL Chi-restraints excluded: chain BE residue 41 ILE Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CB residue 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.132399 restraints weight = 12496.449| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 8.10 r_work: 0.3466 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3955 Z= 0.153 Angle : 0.462 5.323 5325 Z= 0.235 Chirality : 0.054 0.139 600 Planarity : 0.002 0.009 675 Dihedral : 11.457 85.491 565 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.78 % Allowed : 14.32 % Favored : 81.89 % 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: -2.35 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISCC 6 PHE 0.013 0.001 PHEBB 19 TYR 0.014 0.002 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00187 ( 20) link_TRANS : angle 0.44055 ( 60) covalent geometry : bond 0.00354 ( 3935) covalent geometry : angle 0.46174 ( 5265) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.377 Fit side-chains REVERT: C 11 GLU cc_start: 0.7915 (tt0) cc_final: 0.7628 (tt0) REVERT: C 34 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 11 GLU cc_start: 0.7918 (tt0) cc_final: 0.7660 (tt0) REVERT: A 34 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8604 (tt) REVERT: B 11 GLU cc_start: 0.8251 (tt0) cc_final: 0.8004 (tt0) REVERT: D 34 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8355 (tt) REVERT: E 11 GLU cc_start: 0.7994 (tt0) cc_final: 0.7757 (tt0) REVERT: E 34 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8283 (tt) REVERT: BB 35 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8413 (tpt) REVERT: BA 36 VAL cc_start: 0.8528 (t) cc_final: 0.8196 (m) outliers start: 14 outliers final: 4 residues processed: 75 average time/residue: 0.8240 time to fit residues: 64.6987 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CD residue 17 LEU Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.0000 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.177835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.131444 restraints weight = 11105.102| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 7.84 r_work: 0.3467 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3955 Z= 0.184 Angle : 0.477 4.637 5325 Z= 0.245 Chirality : 0.055 0.139 600 Planarity : 0.002 0.011 675 Dihedral : 11.411 87.989 565 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.32 % Allowed : 13.78 % Favored : 81.89 % 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: -2.39 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISCB 6 PHE 0.018 0.002 PHEBB 19 TYR 0.017 0.002 TYR C 10 ARG 0.002 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00222 ( 20) link_TRANS : angle 0.45409 ( 60) covalent geometry : bond 0.00426 ( 3935) covalent geometry : angle 0.47717 ( 5265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.481 Fit side-chains REVERT: C 11 GLU cc_start: 0.7933 (tt0) cc_final: 0.7648 (tt0) REVERT: C 34 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 11 GLU cc_start: 0.7871 (tt0) cc_final: 0.7609 (tt0) REVERT: A 34 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8655 (tt) REVERT: B 11 GLU cc_start: 0.8262 (tt0) cc_final: 0.8020 (tt0) REVERT: D 28 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8107 (mptp) REVERT: D 34 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8395 (tt) REVERT: E 11 GLU cc_start: 0.7996 (tt0) cc_final: 0.7755 (tt0) REVERT: E 34 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8334 (tt) REVERT: BB 35 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8565 (tpt) REVERT: BA 36 VAL cc_start: 0.8578 (t) cc_final: 0.8241 (m) REVERT: CB 35 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7538 (tmm) outliers start: 16 outliers final: 5 residues processed: 79 average time/residue: 0.8347 time to fit residues: 68.9906 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BE residue 18 VAL Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CB residue 35 MET Chi-restraints excluded: chain CD residue 17 LEU Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.133253 restraints weight = 12269.171| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 7.01 r_work: 0.3483 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3955 Z= 0.132 Angle : 0.431 4.317 5325 Z= 0.221 Chirality : 0.054 0.137 600 Planarity : 0.002 0.008 675 Dihedral : 11.174 88.866 565 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.51 % Allowed : 14.59 % Favored : 81.89 % 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: -2.28 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCB 6 PHE 0.014 0.001 PHEBB 19 TYR 0.013 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00171 ( 20) link_TRANS : angle 0.39587 ( 60) covalent geometry : bond 0.00306 ( 3935) covalent geometry : angle 0.43128 ( 5265) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.416 Fit side-chains REVERT: C 11 GLU cc_start: 0.7918 (tt0) cc_final: 0.7627 (tt0) REVERT: C 34 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 11 GLU cc_start: 0.7852 (tt0) cc_final: 0.7592 (tt0) REVERT: A 34 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 11 GLU cc_start: 0.8269 (tt0) cc_final: 0.8056 (tt0) REVERT: D 28 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8136 (mptp) REVERT: D 34 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8473 (tt) REVERT: E 11 GLU cc_start: 0.8079 (tt0) cc_final: 0.7846 (tt0) REVERT: E 34 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8391 (tt) REVERT: BE 35 MET cc_start: 0.7766 (tpt) cc_final: 0.7441 (mmm) REVERT: BC 35 MET cc_start: 0.8296 (tpt) cc_final: 0.7613 (ttt) REVERT: BB 35 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8485 (tpt) REVERT: BA 36 VAL cc_start: 0.8579 (t) cc_final: 0.8229 (m) outliers start: 13 outliers final: 3 residues processed: 79 average time/residue: 0.8794 time to fit residues: 72.4807 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0070 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BB 15 GLN BA 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.178807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.132290 restraints weight = 17944.066| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 9.50 r_work: 0.3459 rms_B_bonded: 6.42 restraints_weight: 2.0000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3955 Z= 0.183 Angle : 0.483 7.499 5325 Z= 0.245 Chirality : 0.054 0.139 600 Planarity : 0.002 0.010 675 Dihedral : 11.377 85.291 565 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.32 % Allowed : 15.95 % Favored : 79.73 % 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: -2.35 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISCC 6 PHE 0.018 0.002 PHEBB 19 TYR 0.019 0.002 TYR C 10 ARG 0.002 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00218 ( 20) link_TRANS : angle 0.43995 ( 60) covalent geometry : bond 0.00424 ( 3935) covalent geometry : angle 0.48310 ( 5265) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.382 Fit side-chains REVERT: C 34 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8430 (tt) REVERT: A 11 GLU cc_start: 0.7831 (tt0) cc_final: 0.7584 (tt0) REVERT: A 34 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (tt) REVERT: B 11 GLU cc_start: 0.8297 (tt0) cc_final: 0.8077 (tt0) REVERT: D 28 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8152 (mptp) REVERT: D 34 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8416 (tt) REVERT: E 11 GLU cc_start: 0.8075 (tt0) cc_final: 0.7853 (tt0) REVERT: E 34 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8370 (tt) REVERT: BE 35 MET cc_start: 0.7697 (tpt) cc_final: 0.7465 (mmm) REVERT: BC 35 MET cc_start: 0.8365 (tpt) cc_final: 0.7712 (ttt) REVERT: BB 35 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8534 (tpt) REVERT: BA 36 VAL cc_start: 0.8577 (t) cc_final: 0.8204 (m) REVERT: CB 35 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7188 (tmm) outliers start: 16 outliers final: 5 residues processed: 80 average time/residue: 0.9151 time to fit residues: 76.3134 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BE residue 18 VAL Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BC residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CB residue 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.0010 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BB 15 GLN BA 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.205647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.151485 restraints weight = 14019.908| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 8.68 r_work: 0.3563 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3955 Z= 0.110 Angle : 0.451 7.226 5325 Z= 0.223 Chirality : 0.054 0.135 600 Planarity : 0.001 0.007 675 Dihedral : 11.058 84.454 565 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.97 % Allowed : 18.11 % Favored : 78.92 % 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: -2.20 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCC 6 PHE 0.012 0.001 PHEBE 19 TYR 0.012 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00143 ( 20) link_TRANS : angle 0.38103 ( 60) covalent geometry : bond 0.00258 ( 3935) covalent geometry : angle 0.45215 ( 5265) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.377 Fit side-chains REVERT: C 11 GLU cc_start: 0.7871 (tt0) cc_final: 0.7595 (tt0) REVERT: C 34 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 11 GLU cc_start: 0.7760 (tt0) cc_final: 0.7511 (tt0) REVERT: A 34 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8538 (tt) REVERT: B 11 GLU cc_start: 0.8189 (tt0) cc_final: 0.7962 (tt0) REVERT: D 34 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8378 (tt) REVERT: E 11 GLU cc_start: 0.8051 (tt0) cc_final: 0.7823 (tt0) REVERT: E 34 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8307 (tt) REVERT: BC 35 MET cc_start: 0.8346 (tpt) cc_final: 0.7735 (ttt) REVERT: BB 35 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8380 (tpt) REVERT: CB 34 LEU cc_start: 0.8580 (tt) cc_final: 0.8332 (tt) REVERT: CB 35 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7072 (tmm) outliers start: 11 outliers final: 3 residues processed: 74 average time/residue: 0.8922 time to fit residues: 68.8803 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CB residue 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BB 15 GLN BA 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.178814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.132668 restraints weight = 13403.902| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 7.57 r_work: 0.3473 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3955 Z= 0.150 Angle : 0.487 7.230 5325 Z= 0.243 Chirality : 0.054 0.136 600 Planarity : 0.002 0.008 675 Dihedral : 10.970 85.087 565 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.97 % Allowed : 18.92 % Favored : 78.11 % 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: -2.22 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISCD 6 PHE 0.014 0.001 PHEBB 19 TYR 0.015 0.002 TYR C 10 ARG 0.002 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 20) link_TRANS : angle 0.38581 ( 60) covalent geometry : bond 0.00355 ( 3935) covalent geometry : angle 0.48821 ( 5265) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.439 Fit side-chains REVERT: C 11 GLU cc_start: 0.7853 (tt0) cc_final: 0.7586 (tt0) REVERT: C 34 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8432 (tt) REVERT: A 11 GLU cc_start: 0.7763 (tt0) cc_final: 0.7513 (tt0) REVERT: A 34 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 11 GLU cc_start: 0.8240 (tt0) cc_final: 0.8039 (tt0) REVERT: D 34 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (tt) REVERT: E 11 GLU cc_start: 0.8064 (tt0) cc_final: 0.7851 (tt0) REVERT: E 34 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8347 (tt) REVERT: BC 35 MET cc_start: 0.8406 (tpt) cc_final: 0.7677 (ttt) REVERT: BB 35 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8540 (tpt) REVERT: BA 16 LYS cc_start: 0.5883 (ttmt) cc_final: 0.5450 (ttpp) REVERT: CB 35 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7211 (tmm) outliers start: 11 outliers final: 3 residues processed: 73 average time/residue: 0.8967 time to fit residues: 68.3402 Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain BD residue 18 VAL Chi-restraints excluded: chain BD residue 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CB residue 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BB 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.178172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.131041 restraints weight = 13447.208| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 8.33 r_work: 0.3493 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3955 Z= 0.203 Angle : 0.531 7.076 5325 Z= 0.268 Chirality : 0.055 0.139 600 Planarity : 0.002 0.012 675 Dihedral : 11.176 86.901 565 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.51 % Allowed : 18.92 % Favored : 77.57 % 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: -2.29 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISCB 6 PHE 0.018 0.002 PHEBB 19 TYR 0.020 0.002 TYR C 10 ARG 0.003 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00252 ( 20) link_TRANS : angle 0.46241 ( 60) covalent geometry : bond 0.00470 ( 3935) covalent geometry : angle 0.53136 ( 5265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4192.91 seconds wall clock time: 72 minutes 56.07 seconds (4376.07 seconds total)