Starting phenix.real_space_refine on Fri May 9 21:02:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb2_61305/05_2025/9jb2_61305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb2_61305/05_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_61305/05_2025/9jb2_61305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb2_61305/05_2025/9jb2_61305.map" model { file = "/net/cci-nas-00/data/ceres_data/9jb2_61305/05_2025/9jb2_61305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb2_61305/05_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-5687/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: 3.49, per 1000 atoms: 0.90 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: 0.88 Conformation dependent library (CDL) restraints added in 465.1 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: 0.65 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: 1.03 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- 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: 1.0711 time to fit residues: 95.3207 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 : 0.353 ------------------------------------------------------------------------------- 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 = 0.129091 restraints weight = 16307.566| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 8.20 r_work: 0.3441 rms_B_bonded: 5.84 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 = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- 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 : 0.433 Fit side-chains REVERT: C 11 GLU cc_start: 0.7892 (tt0) cc_final: 0.7601 (tt0) REVERT: A 11 GLU cc_start: 0.7919 (tt0) cc_final: 0.7634 (tt0) REVERT: A 34 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8585 (tt) REVERT: B 11 GLU cc_start: 0.8252 (tt0) cc_final: 0.7968 (tt0) REVERT: E 11 GLU cc_start: 0.8133 (tt0) cc_final: 0.7869 (tt0) REVERT: BE 35 MET cc_start: 0.8316 (tpt) cc_final: 0.7918 (tpt) REVERT: BD 15 GLN cc_start: 0.4895 (mt0) cc_final: 0.4689 (mt0) REVERT: BB 35 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8557 (tpt) outliers start: 12 outliers final: 1 residues processed: 79 average time/residue: 0.9838 time to fit residues: 80.8408 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 : 0.407 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.177025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.128409 restraints weight = 14330.789| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 8.21 r_work: 0.3456 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3955 Z= 0.146 Angle : 0.417 5.800 5325 Z= 0.218 Chirality : 0.054 0.138 600 Planarity : 0.002 0.006 675 Dihedral : 10.668 80.186 565 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.05 % Allowed : 10.81 % Favored : 85.14 % 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: -2.14 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCB 6 PHE 0.013 0.001 PHEBB 19 TYR 0.011 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00165 ( 20) link_TRANS : angle 0.39216 ( 60) covalent geometry : bond 0.00335 ( 3935) covalent geometry : angle 0.41678 ( 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.403 Fit side-chains REVERT: C 11 GLU cc_start: 0.7869 (tt0) cc_final: 0.7583 (tt0) REVERT: C 34 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 11 GLU cc_start: 0.7921 (tt0) cc_final: 0.7647 (tt0) REVERT: A 34 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 11 GLU cc_start: 0.8207 (tt0) cc_final: 0.7935 (tt0) REVERT: B 34 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8468 (tt) REVERT: D 34 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8440 (tt) REVERT: E 11 GLU cc_start: 0.8085 (tt0) cc_final: 0.7817 (tt0) REVERT: BE 35 MET cc_start: 0.8194 (tpt) cc_final: 0.7764 (tpt) REVERT: BD 15 GLN cc_start: 0.4884 (mt0) cc_final: 0.4658 (mt0) REVERT: BC 35 MET cc_start: 0.8501 (tpt) cc_final: 0.7688 (ttt) REVERT: BB 35 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8433 (tpt) outliers start: 15 outliers final: 4 residues processed: 79 average time/residue: 0.8758 time to fit residues: 72.2575 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain D 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 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: 1.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.176823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.128690 restraints weight = 15272.790| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 7.95 r_work: 0.3451 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3955 Z= 0.162 Angle : 0.438 5.322 5325 Z= 0.227 Chirality : 0.054 0.140 600 Planarity : 0.002 0.008 675 Dihedral : 11.228 89.649 565 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.78 % Allowed : 12.16 % Favored : 84.05 % 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: -2.18 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 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 0.00192 ( 20) link_TRANS : angle 0.40836 ( 60) covalent geometry : bond 0.00372 ( 3935) covalent geometry : angle 0.43874 ( 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 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.393 Fit side-chains REVERT: C 11 GLU cc_start: 0.7906 (tt0) cc_final: 0.7618 (tt0) REVERT: C 34 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 11 GLU cc_start: 0.7914 (tt0) cc_final: 0.7667 (tt0) REVERT: A 34 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8602 (tt) REVERT: B 11 GLU cc_start: 0.8231 (tt0) cc_final: 0.7990 (tt0) REVERT: B 34 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8511 (tt) REVERT: D 34 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8461 (tt) REVERT: E 11 GLU cc_start: 0.8080 (tt0) cc_final: 0.7822 (tt0) REVERT: E 34 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8350 (tt) REVERT: BE 35 MET cc_start: 0.8203 (tpt) cc_final: 0.7803 (tpt) REVERT: BD 15 GLN cc_start: 0.4983 (mt0) cc_final: 0.4766 (mt0) REVERT: BB 35 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8412 (tpt) REVERT: CB 35 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8062 (tmm) REVERT: CE 11 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7649 (mt-10) outliers start: 14 outliers final: 4 residues processed: 76 average time/residue: 0.8540 time to fit residues: 67.9050 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU 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 CE residue 11 GLU 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.175266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127513 restraints weight = 12574.674| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 7.37 r_work: 0.3426 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3955 Z= 0.208 Angle : 0.483 4.892 5325 Z= 0.251 Chirality : 0.055 0.142 600 Planarity : 0.002 0.012 675 Dihedral : 11.481 84.763 565 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 : 4.59 % Allowed : 12.16 % Favored : 83.24 % 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: -2.30 (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 HISCC 6 PHE 0.015 0.002 PHEBB 19 TYR 0.018 0.002 TYR C 10 ARG 0.002 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00253 ( 20) link_TRANS : angle 0.48550 ( 60) covalent geometry : bond 0.00481 ( 3935) covalent geometry : angle 0.48323 ( 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.374 Fit side-chains REVERT: C 11 GLU cc_start: 0.7901 (tt0) cc_final: 0.7618 (tt0) REVERT: C 34 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 11 GLU cc_start: 0.7908 (tt0) cc_final: 0.7648 (tt0) REVERT: A 34 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8664 (tt) REVERT: B 11 GLU cc_start: 0.8223 (tt0) cc_final: 0.8001 (tt0) REVERT: B 34 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (tt) REVERT: D 34 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8433 (tt) REVERT: E 11 GLU cc_start: 0.8058 (tt0) cc_final: 0.7813 (tt0) REVERT: E 34 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8368 (tt) REVERT: CC 26 SER cc_start: 0.8187 (m) cc_final: 0.7717 (t) REVERT: BB 35 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8640 (tpt) REVERT: BA 36 VAL cc_start: 0.8526 (t) cc_final: 0.8159 (m) REVERT: CB 35 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7968 (tmm) outliers start: 17 outliers final: 5 residues processed: 75 average time/residue: 0.8303 time to fit residues: 65.0554 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 overall best weight: 1.0400 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.177328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.130614 restraints weight = 11088.879| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 7.70 r_work: 0.3458 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3955 Z= 0.201 Angle : 0.476 4.650 5325 Z= 0.248 Chirality : 0.055 0.140 600 Planarity : 0.002 0.011 675 Dihedral : 11.519 89.217 565 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.59 % Allowed : 12.43 % Favored : 82.97 % 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: -2.34 (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 0.021 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 0.00238 ( 20) link_TRANS : angle 0.47817 ( 60) covalent geometry : bond 0.00465 ( 3935) covalent geometry : angle 0.47553 ( 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 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.389 Fit side-chains REVERT: C 11 GLU cc_start: 0.7932 (tt0) cc_final: 0.7652 (tt0) REVERT: C 34 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 11 GLU cc_start: 0.7843 (tt0) cc_final: 0.7583 (tt0) REVERT: A 34 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 11 GLU cc_start: 0.8243 (tt0) cc_final: 0.8019 (tt0) REVERT: B 34 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8488 (tt) REVERT: D 34 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8384 (tt) REVERT: E 11 GLU cc_start: 0.8061 (tt0) cc_final: 0.7827 (tt0) REVERT: E 34 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8322 (tt) REVERT: BE 35 MET cc_start: 0.8170 (tpt) cc_final: 0.7796 (tpt) REVERT: BB 35 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (tpt) REVERT: BA 36 VAL cc_start: 0.8507 (t) cc_final: 0.8195 (m) REVERT: CB 35 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7902 (tmm) outliers start: 17 outliers final: 6 residues processed: 77 average time/residue: 0.8093 time to fit residues: 65.2604 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 34 LEU 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 Chi-restraints excluded: chain CE residue 35 MET 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: 0.9980 chunk 37 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.179059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.132396 restraints weight = 12229.567| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 7.83 r_work: 0.3492 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3955 Z= 0.117 Angle : 0.408 5.006 5325 Z= 0.213 Chirality : 0.054 0.138 600 Planarity : 0.001 0.008 675 Dihedral : 11.210 88.275 565 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.78 % Allowed : 13.24 % Favored : 82.97 % 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: -2.25 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCC 6 PHE 0.011 0.001 PHEBB 19 TYR 0.012 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00147 ( 20) link_TRANS : angle 0.38562 ( 60) covalent geometry : bond 0.00275 ( 3935) covalent geometry : angle 0.40778 ( 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.395 Fit side-chains REVERT: C 11 GLU cc_start: 0.7867 (tt0) cc_final: 0.7582 (tt0) REVERT: C 34 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 11 GLU cc_start: 0.7837 (tt0) cc_final: 0.7577 (tt0) REVERT: A 34 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 11 GLU cc_start: 0.8225 (tt0) cc_final: 0.7993 (tt0) REVERT: D 34 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8410 (tt) REVERT: E 11 GLU cc_start: 0.8048 (tt0) cc_final: 0.7820 (tt0) REVERT: E 34 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8349 (tt) REVERT: BE 35 MET cc_start: 0.7886 (tpt) cc_final: 0.7544 (tpt) REVERT: BC 35 MET cc_start: 0.8263 (tpt) cc_final: 0.7537 (ttt) REVERT: BB 35 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8415 (tpt) REVERT: BA 36 VAL cc_start: 0.8521 (t) cc_final: 0.8177 (m) outliers start: 14 outliers final: 3 residues processed: 79 average time/residue: 0.8168 time to fit residues: 67.4979 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.179120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.131494 restraints weight = 17827.526| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 8.88 r_work: 0.3462 rms_B_bonded: 6.32 restraints_weight: 2.0000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 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 = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3955 Z= 0.135 Angle : 0.456 7.424 5325 Z= 0.227 Chirality : 0.054 0.137 600 Planarity : 0.002 0.008 675 Dihedral : 11.086 85.718 565 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.78 % Allowed : 15.41 % Favored : 80.81 % 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: -2.24 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCB 6 PHE 0.015 0.001 PHEBB 19 TYR 0.014 0.001 TYR C 10 ARG 0.002 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00169 ( 20) link_TRANS : angle 0.37845 ( 60) covalent geometry : bond 0.00316 ( 3935) covalent geometry : angle 0.45685 ( 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.369 Fit side-chains REVERT: C 11 GLU cc_start: 0.7891 (tt0) cc_final: 0.7631 (tt0) REVERT: C 34 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8441 (tt) REVERT: A 11 GLU cc_start: 0.7832 (tt0) cc_final: 0.7573 (tt0) REVERT: A 34 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 11 GLU cc_start: 0.8254 (tt0) cc_final: 0.8035 (tt0) REVERT: D 28 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8107 (mptp) REVERT: D 34 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8447 (tt) REVERT: E 11 GLU cc_start: 0.8071 (tt0) cc_final: 0.7835 (tt0) REVERT: E 34 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8377 (tt) REVERT: BE 35 MET cc_start: 0.7846 (tpt) cc_final: 0.7495 (tpt) REVERT: BC 35 MET cc_start: 0.8169 (tpt) cc_final: 0.7632 (ttt) REVERT: BB 35 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8467 (tpt) REVERT: BA 36 VAL cc_start: 0.8555 (t) cc_final: 0.8219 (m) outliers start: 14 outliers final: 4 residues processed: 78 average time/residue: 0.8949 time to fit residues: 72.7477 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 BC residue 41 ILE Chi-restraints excluded: chain BB 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: 0.4980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.190073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.142302 restraints weight = 14458.436| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 9.54 r_work: 0.3555 rms_B_bonded: 6.36 restraints_weight: 2.0000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3955 Z= 0.106 Angle : 0.444 6.998 5325 Z= 0.219 Chirality : 0.054 0.135 600 Planarity : 0.001 0.008 675 Dihedral : 10.865 83.669 565 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.78 % Allowed : 15.95 % Favored : 80.27 % 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: -2.21 (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 HISCB 6 PHE 0.011 0.001 PHEBB 19 TYR 0.012 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00139 ( 20) link_TRANS : angle 0.34980 ( 60) covalent geometry : bond 0.00252 ( 3935) covalent geometry : angle 0.44509 ( 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 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.371 Fit side-chains REVERT: C 11 GLU cc_start: 0.7877 (tt0) cc_final: 0.7607 (tt0) REVERT: C 34 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8327 (tt) REVERT: A 11 GLU cc_start: 0.7814 (tt0) cc_final: 0.7570 (tt0) REVERT: A 34 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8515 (tt) REVERT: B 11 GLU cc_start: 0.8236 (tt0) cc_final: 0.8003 (tt0) REVERT: D 28 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8077 (mptp) REVERT: D 34 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8418 (tt) REVERT: E 11 GLU cc_start: 0.8043 (tt0) cc_final: 0.7840 (tt0) REVERT: E 34 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8369 (tt) REVERT: BE 35 MET cc_start: 0.7664 (tpt) cc_final: 0.7427 (mmm) REVERT: BC 35 MET cc_start: 0.8068 (tpt) cc_final: 0.7536 (ttt) REVERT: BB 35 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8441 (tpt) REVERT: BA 16 LYS cc_start: 0.6109 (ttmt) cc_final: 0.5551 (ttpp) REVERT: BA 36 VAL cc_start: 0.8544 (t) cc_final: 0.8202 (m) REVERT: CB 35 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7538 (tmm) outliers start: 14 outliers final: 3 residues processed: 76 average time/residue: 0.8733 time to fit residues: 69.2532 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0170 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.190983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.143634 restraints weight = 13178.015| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 8.72 r_work: 0.3574 rms_B_bonded: 6.18 restraints_weight: 2.0000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3955 Z= 0.113 Angle : 0.454 6.913 5325 Z= 0.225 Chirality : 0.054 0.134 600 Planarity : 0.001 0.005 675 Dihedral : 10.675 81.449 565 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.97 % Allowed : 17.30 % 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: -2.19 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCB 6 PHE 0.011 0.001 PHEBB 19 TYR 0.012 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00145 ( 20) link_TRANS : angle 0.33589 ( 60) covalent geometry : bond 0.00268 ( 3935) covalent geometry : angle 0.45488 ( 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 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.365 Fit side-chains REVERT: C 11 GLU cc_start: 0.7865 (tt0) cc_final: 0.7599 (tt0) REVERT: C 34 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 11 GLU cc_start: 0.7784 (tt0) cc_final: 0.7536 (tt0) REVERT: A 34 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8513 (tt) REVERT: B 11 GLU cc_start: 0.8190 (tt0) cc_final: 0.7939 (tt0) REVERT: D 28 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8058 (mptp) REVERT: D 34 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8408 (tt) REVERT: E 11 GLU cc_start: 0.8039 (tt0) cc_final: 0.7838 (tt0) REVERT: E 34 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8355 (tt) REVERT: BE 35 MET cc_start: 0.7508 (tpt) cc_final: 0.7230 (mmm) REVERT: BC 35 MET cc_start: 0.8206 (tpt) cc_final: 0.7608 (ttt) REVERT: BB 35 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8539 (tpt) REVERT: BA 16 LYS cc_start: 0.5952 (ttmt) cc_final: 0.5548 (ttpp) REVERT: BA 36 VAL cc_start: 0.8525 (t) cc_final: 0.8176 (m) REVERT: CB 34 LEU cc_start: 0.8538 (tt) cc_final: 0.8281 (tt) REVERT: CB 35 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7471 (tmm) REVERT: CD 35 MET cc_start: 0.7848 (ttt) cc_final: 0.7538 (tpp) outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.9466 time to fit residues: 74.9163 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.0000 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.0470 chunk 5 optimal weight: 0.7980 overall best weight: 0.3340 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.192642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.145064 restraints weight = 13280.366| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 8.82 r_work: 0.3593 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3955 Z= 0.099 Angle : 0.442 6.872 5325 Z= 0.218 Chirality : 0.054 0.134 600 Planarity : 0.001 0.005 675 Dihedral : 10.435 81.817 565 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.97 % Allowed : 17.30 % 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: -2.12 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISCC 6 PHE 0.007 0.001 PHEBB 19 TYR 0.011 0.001 TYR C 10 ARG 0.001 0.000 ARGCE 5 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 20) link_TRANS : angle 0.30636 ( 60) covalent geometry : bond 0.00233 ( 3935) covalent geometry : angle 0.44376 ( 5265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.70 seconds wall clock time: 60 minutes 4.20 seconds (3604.20 seconds total)