Starting phenix.real_space_refine on Wed Sep 17 04:10:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb2_61305/09_2025/9jb2_61305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb2_61305/09_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_61305/09_2025/9jb2_61305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb2_61305/09_2025/9jb2_61305.map" model { file = "/net/cci-nas-00/data/ceres_data/9jb2_61305/09_2025/9jb2_61305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb2_61305/09_2025/9jb2_61305.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.36, per 1000 atoms: 0.35 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: 0.31 Conformation dependent library (CDL) restraints added in 168.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.39 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: 0.44 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 18 or resid 20 through 42)) selection = (chain 'B' and (resid 9 through 18 or resid 20 through 42)) selection = (chain 'C' and (resid 9 through 18 or resid 20 through 42)) selection = (chain 'D' and (resid 9 through 18 or resid 20 through 42)) selection = (chain 'E' and (resid 9 through 18 or resid 20 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: 2.350 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.850 Find NCS groups from input model: 0.110 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:8.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- 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 : 5.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARGCA 5 TYR 0.008 0.001 TYRCB 10 PHE 0.010 0.001 PHE D 20 HIS 0.003 0.001 HISCA 14 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3935) covalent geometry : angle 0.42923 ( 5265) link_TRANS : bond 0.00143 ( 20) link_TRANS : angle 0.40643 ( 60) *********************** 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 : 0.141 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: 0.7970 (tt0) REVERT: E 11 GLU cc_start: 0.8045 (tt0) cc_final: 0.7792 (tt0) REVERT: E 34 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8495 (tt) REVERT: BE 35 MET cc_start: 0.8639 (tpt) cc_final: 0.8269 (tpt) REVERT: BD 15 GLN cc_start: 0.5776 (mt0) cc_final: 0.5343 (mt0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.5407 time to fit residues: 48.0571 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 : 0.151 ------------------------------------------------------------------------------- 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 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.175033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.127142 restraints weight = 14260.835| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 7.83 r_work: 0.3429 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0710 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 : 0.436 5.447 5325 Z= 0.227 Chirality : 0.054 0.138 600 Planarity : 0.002 0.009 675 Dihedral : 9.950 74.487 567 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.32 % Allowed : 9.73 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARGCE 5 TYR 0.008 0.001 TYRCB 10 PHE 0.017 0.001 PHEBB 19 HIS 0.003 0.001 HISCC 6 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3935) covalent geometry : angle 0.43658 ( 5265) link_TRANS : bond 0.00166 ( 20) link_TRANS : angle 0.42586 ( 60) *********************** 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.142 Fit side-chains REVERT: C 11 GLU cc_start: 0.7908 (tt0) cc_final: 0.7619 (tt0) REVERT: A 11 GLU cc_start: 0.7963 (tt0) cc_final: 0.7694 (tt0) REVERT: A 34 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8604 (tt) REVERT: B 11 GLU cc_start: 0.8238 (tt0) cc_final: 0.7958 (tt0) REVERT: E 11 GLU cc_start: 0.8130 (tt0) cc_final: 0.7867 (tt0) REVERT: BE 35 MET cc_start: 0.8343 (tpt) cc_final: 0.7923 (tpt) REVERT: BD 15 GLN cc_start: 0.4885 (mt0) cc_final: 0.4645 (mt0) REVERT: BB 35 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8477 (tpt) REVERT: CD 35 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7902 (ttt) outliers start: 16 outliers final: 3 residues processed: 79 average time/residue: 0.4655 time to fit residues: 38.2554 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 35 MET Chi-restraints excluded: chain CE residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.177292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.129081 restraints weight = 16529.436| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 8.33 r_work: 0.3441 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3441 ------------------------------------------------------------------------------- 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 = 0.42 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: 0.7816 moved from start: 0.0973 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= 0.147 Angle : 0.419 5.400 5325 Z= 0.218 Chirality : 0.054 0.137 600 Planarity : 0.002 0.006 675 Dihedral : 10.761 81.144 565 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGCE 5 TYR 0.012 0.002 TYR C 10 PHE 0.013 0.001 PHEBB 19 HIS 0.003 0.001 HISCB 6 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3935) covalent geometry : angle 0.41941 ( 5265) link_TRANS : bond 0.00170 ( 20) link_TRANS : angle 0.40203 ( 60) *********************** 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.155 Fit side-chains REVERT: C 11 GLU cc_start: 0.7918 (tt0) cc_final: 0.7621 (tt0) REVERT: C 34 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 11 GLU cc_start: 0.7948 (tt0) cc_final: 0.7684 (tt0) REVERT: A 34 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 11 GLU cc_start: 0.8226 (tt0) cc_final: 0.7951 (tt0) REVERT: B 34 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8494 (tt) REVERT: D 34 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (tt) REVERT: E 11 GLU cc_start: 0.8131 (tt0) cc_final: 0.7849 (tt0) REVERT: E 34 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8343 (tt) REVERT: BE 35 MET cc_start: 0.8225 (tpt) cc_final: 0.7807 (tpt) REVERT: BD 15 GLN cc_start: 0.5029 (mt0) cc_final: 0.4787 (mt0) REVERT: BC 35 MET cc_start: 0.8510 (tpt) cc_final: 0.7688 (ttt) REVERT: BB 35 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8394 (tpt) REVERT: CB 35 MET cc_start: 0.8216 (ttt) cc_final: 0.8008 (tmm) REVERT: CD 35 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7934 (ttt) outliers start: 14 outliers final: 3 residues processed: 76 average time/residue: 0.4004 time to fit residues: 31.8082 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CD 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 2 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 32 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.178000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.130966 restraints weight = 13418.328| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 7.82 r_work: 0.3474 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 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 = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3955 Z= 0.127 Angle : 0.409 4.830 5325 Z= 0.211 Chirality : 0.054 0.137 600 Planarity : 0.002 0.008 675 Dihedral : 11.044 89.926 565 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 4.05 % Allowed : 12.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARGCE 5 TYR 0.012 0.001 TYR C 10 PHE 0.011 0.001 PHEBE 19 HIS 0.003 0.001 HISCB 6 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3935) covalent geometry : angle 0.40970 ( 5265) link_TRANS : bond 0.00155 ( 20) link_TRANS : angle 0.37040 ( 60) *********************** 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 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.138 Fit side-chains REVERT: C 11 GLU cc_start: 0.7881 (tt0) cc_final: 0.7589 (tt0) REVERT: C 34 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 11 GLU cc_start: 0.7921 (tt0) cc_final: 0.7674 (tt0) REVERT: A 34 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8560 (tt) REVERT: B 11 GLU cc_start: 0.8208 (tt0) cc_final: 0.7939 (tt0) REVERT: B 34 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8487 (tt) REVERT: E 11 GLU cc_start: 0.8070 (tt0) cc_final: 0.7849 (tt0) REVERT: E 34 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8357 (tt) REVERT: BE 35 MET cc_start: 0.8120 (tpt) cc_final: 0.7715 (tpt) REVERT: BC 28 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7228 (mtmt) REVERT: BB 35 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8482 (tpt) REVERT: CD 35 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7954 (ttt) outliers start: 15 outliers final: 4 residues processed: 78 average time/residue: 0.4271 time to fit residues: 34.7082 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 28 LYS Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CD 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 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.177991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.131581 restraints weight = 13708.767| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 7.93 r_work: 0.3492 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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: 0.7827 moved from start: 0.1274 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= 0.137 Angle : 0.419 5.197 5325 Z= 0.215 Chirality : 0.054 0.137 600 Planarity : 0.002 0.006 675 Dihedral : 10.898 83.600 565 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.78 % Allowed : 14.86 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGCE 5 TYR 0.013 0.001 TYR C 10 PHE 0.010 0.001 PHEBB 19 HIS 0.003 0.001 HISCC 6 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3935) covalent geometry : angle 0.41964 ( 5265) link_TRANS : bond 0.00177 ( 20) link_TRANS : angle 0.36823 ( 60) *********************** 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 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.143 Fit side-chains REVERT: C 11 GLU cc_start: 0.7927 (tt0) cc_final: 0.7632 (tt0) REVERT: C 34 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 11 GLU cc_start: 0.7944 (tt0) cc_final: 0.7686 (tt0) REVERT: A 34 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8580 (tt) REVERT: B 11 GLU cc_start: 0.8263 (tt0) cc_final: 0.8002 (tt0) REVERT: E 11 GLU cc_start: 0.8114 (tt0) cc_final: 0.7890 (tt0) REVERT: E 34 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8414 (tt) REVERT: BE 35 MET cc_start: 0.8180 (tpt) cc_final: 0.7842 (tpt) REVERT: BB 35 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8557 (tpt) REVERT: CD 35 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7987 (ttt) outliers start: 14 outliers final: 4 residues processed: 75 average time/residue: 0.4181 time to fit residues: 32.6941 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 : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A 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 CD residue 35 MET 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 23 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.2764 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.181715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.136221 restraints weight = 13018.737| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 7.81 r_work: 0.3550 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3955 Z= 0.089 Angle : 0.393 6.535 5325 Z= 0.198 Chirality : 0.054 0.136 600 Planarity : 0.001 0.005 675 Dihedral : 10.601 80.753 565 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.70 % Allowed : 15.68 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.000 0.000 ARGCE 5 TYR 0.009 0.001 TYR C 10 PHE 0.007 0.001 PHEBE 19 HIS 0.003 0.001 HISCB 6 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 3935) covalent geometry : angle 0.39352 ( 5265) link_TRANS : bond 0.00113 ( 20) link_TRANS : angle 0.31439 ( 60) *********************** 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 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.144 Fit side-chains REVERT: C 11 GLU cc_start: 0.7905 (tt0) cc_final: 0.7629 (tt0) REVERT: C 34 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 34 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8478 (tt) REVERT: B 11 GLU cc_start: 0.8264 (tt0) cc_final: 0.8015 (tt0) REVERT: D 34 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8532 (tt) REVERT: E 11 GLU cc_start: 0.8099 (tt0) cc_final: 0.7869 (tt0) REVERT: E 34 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8426 (tt) REVERT: BC 35 MET cc_start: 0.8370 (tpt) cc_final: 0.7742 (ttt) REVERT: BB 35 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8466 (tpt) REVERT: CB 35 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7658 (tmm) outliers start: 10 outliers final: 1 residues processed: 75 average time/residue: 0.4575 time to fit residues: 35.6824 Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 41 ILE Chi-restraints excluded: chain BB residue 35 MET Chi-restraints excluded: chain CB residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.177720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.129468 restraints weight = 15053.537| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 8.17 r_work: 0.3451 rms_B_bonded: 5.92 restraints_weight: 2.0000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 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 = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3955 Z= 0.167 Angle : 0.444 5.517 5325 Z= 0.229 Chirality : 0.054 0.138 600 Planarity : 0.002 0.010 675 Dihedral : 11.006 82.723 565 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.51 % Allowed : 16.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (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 ARG 0.002 0.000 ARGCE 5 TYR 0.016 0.002 TYR C 10 PHE 0.016 0.001 PHEBB 19 HIS 0.004 0.001 HISCC 6 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3935) covalent geometry : angle 0.44410 ( 5265) link_TRANS : bond 0.00213 ( 20) link_TRANS : angle 0.38985 ( 60) *********************** 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 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.146 Fit side-chains REVERT: C 11 GLU cc_start: 0.7871 (tt0) cc_final: 0.7593 (tt0) REVERT: C 34 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 34 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 11 GLU cc_start: 0.8207 (tt0) cc_final: 0.7962 (tt0) REVERT: D 34 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8474 (tt) REVERT: E 11 GLU cc_start: 0.8063 (tt0) cc_final: 0.7859 (tt0) REVERT: E 34 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8382 (tt) REVERT: BE 35 MET cc_start: 0.8165 (tpt) cc_final: 0.7791 (tpt) REVERT: BC 35 MET cc_start: 0.8359 (tpt) cc_final: 0.7723 (ttt) REVERT: BB 35 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8487 (tpt) REVERT: CB 35 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7848 (tmm) outliers start: 13 outliers final: 3 residues processed: 73 average time/residue: 0.4872 time to fit residues: 36.9403 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 : 0.144 ------------------------------------------------------------------------------- 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 CD residue 17 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.179615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.131724 restraints weight = 13424.182| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 7.73 r_work: 0.3479 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1504 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= 0.122 Angle : 0.433 5.353 5325 Z= 0.217 Chirality : 0.054 0.137 600 Planarity : 0.002 0.008 675 Dihedral : 10.914 84.275 565 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.51 % Allowed : 15.41 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.36), 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 ARG 0.001 0.000 ARGCE 5 TYR 0.013 0.001 TYR C 10 PHE 0.013 0.001 PHEBB 19 HIS 0.004 0.001 HISCB 6 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3935) covalent geometry : angle 0.43406 ( 5265) link_TRANS : bond 0.00165 ( 20) link_TRANS : angle 0.34935 ( 60) *********************** 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 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.127 Fit side-chains REVERT: C 11 GLU cc_start: 0.7880 (tt0) cc_final: 0.7605 (tt0) REVERT: C 34 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 34 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8600 (tt) REVERT: B 11 GLU cc_start: 0.8225 (tt0) cc_final: 0.8006 (tt0) REVERT: D 34 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8507 (tt) REVERT: E 11 GLU cc_start: 0.8044 (tt0) cc_final: 0.7836 (tt0) REVERT: E 34 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8413 (tt) REVERT: BC 35 MET cc_start: 0.8361 (tpt) cc_final: 0.7627 (ttt) REVERT: BB 35 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8495 (tpt) REVERT: CB 35 MET cc_start: 0.8007 (tmm) cc_final: 0.7783 (tmm) REVERT: CE 35 MET cc_start: 0.7943 (ttt) cc_final: 0.7602 (ttt) outliers start: 13 outliers final: 4 residues processed: 73 average time/residue: 0.4471 time to fit residues: 33.9210 Evaluate side-chains 72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.0000 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.180958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.133075 restraints weight = 13306.781| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 7.79 r_work: 0.3528 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3955 Z= 0.109 Angle : 0.407 5.201 5325 Z= 0.208 Chirality : 0.054 0.136 600 Planarity : 0.001 0.008 675 Dihedral : 10.810 85.705 565 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.70 % Allowed : 16.22 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGCE 5 TYR 0.012 0.001 TYR C 10 PHE 0.012 0.001 PHEBE 19 HIS 0.003 0.001 HISCB 6 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3935) covalent geometry : angle 0.40798 ( 5265) link_TRANS : bond 0.00143 ( 20) link_TRANS : angle 0.32147 ( 60) *********************** 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 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.141 Fit side-chains REVERT: C 11 GLU cc_start: 0.7884 (tt0) cc_final: 0.7608 (tt0) REVERT: C 34 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 34 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8571 (tt) REVERT: B 11 GLU cc_start: 0.8210 (tt0) cc_final: 0.7998 (tt0) REVERT: E 11 GLU cc_start: 0.8079 (tt0) cc_final: 0.7876 (tt0) REVERT: E 34 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8453 (tt) REVERT: BC 35 MET cc_start: 0.8344 (tpt) cc_final: 0.7575 (ttt) REVERT: BB 34 LEU cc_start: 0.8025 (tp) cc_final: 0.7806 (tp) REVERT: BB 35 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8468 (tpt) REVERT: BA 15 GLN cc_start: 0.5269 (OUTLIER) cc_final: 0.5032 (mp10) REVERT: BA 16 LYS cc_start: 0.6269 (ttmt) cc_final: 0.5713 (ttpp) REVERT: CB 35 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7380 (tmm) REVERT: CE 35 MET cc_start: 0.7965 (ttt) cc_final: 0.7653 (ttt) outliers start: 10 outliers final: 2 residues processed: 69 average time/residue: 0.4994 time to fit residues: 35.7921 Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A 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 BA residue 15 GLN Chi-restraints excluded: chain CB residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.176596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.128334 restraints weight = 12823.029| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 7.98 r_work: 0.3427 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3955 Z= 0.275 Angle : 0.579 5.708 5325 Z= 0.294 Chirality : 0.056 0.149 600 Planarity : 0.003 0.016 675 Dihedral : 11.388 85.196 565 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.97 % Allowed : 16.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGCE 5 TYR 0.024 0.003 TYR C 10 PHE 0.021 0.002 PHEBB 19 HIS 0.005 0.002 HISCC 6 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 3935) covalent geometry : angle 0.57918 ( 5265) link_TRANS : bond 0.00335 ( 20) link_TRANS : angle 0.54870 ( 60) ********************** 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 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.148 Fit side-chains REVERT: C 11 GLU cc_start: 0.7927 (tt0) cc_final: 0.7644 (tt0) REVERT: C 34 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8363 (tt) REVERT: A 34 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8758 (tt) REVERT: B 11 GLU cc_start: 0.8237 (tt0) cc_final: 0.7990 (tt0) REVERT: E 34 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8377 (tt) REVERT: BB 34 LEU cc_start: 0.8101 (tp) cc_final: 0.7870 (tp) REVERT: BB 35 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8504 (tpt) REVERT: BA 15 GLN cc_start: 0.5141 (OUTLIER) cc_final: 0.4796 (mp10) REVERT: BA 16 LYS cc_start: 0.5964 (ttmt) cc_final: 0.5528 (ttpp) REVERT: CB 35 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7679 (tmm) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.4618 time to fit residues: 36.5391 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain A 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 BA residue 15 GLN 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 10 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 12 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.180002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.131077 restraints weight = 14153.995| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 8.00 r_work: 0.3470 rms_B_bonded: 5.93 restraints_weight: 2.0000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 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 = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3955 Z= 0.113 Angle : 0.447 6.561 5325 Z= 0.223 Chirality : 0.055 0.142 600 Planarity : 0.001 0.007 675 Dihedral : 11.055 83.996 565 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.70 % Allowed : 17.84 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGCE 5 TYR 0.013 0.001 TYR C 10 PHE 0.014 0.001 PHEBE 19 HIS 0.003 0.001 HISCC 6 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3935) covalent geometry : angle 0.44741 ( 5265) link_TRANS : bond 0.00141 ( 20) link_TRANS : angle 0.39463 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1762.86 seconds wall clock time: 30 minutes 51.20 seconds (1851.20 seconds total)