Starting phenix.real_space_refine on Wed Aug 5 21:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjt_60156/08_2026/8zjt_60156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjt_60156/08_2026/8zjt_60156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjt_60156/08_2026/8zjt_60156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjt_60156/08_2026/8zjt_60156.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjt_60156/08_2026/8zjt_60156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjt_60156/08_2026/8zjt_60156.cif" } resolution = 3.2 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= 0.002 sd= 0.071 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: 5 Type Number sf(0) Gaussians P 278 5.49 5 S 10 5.16 5 C 6534 2.51 5 N 2228 2.21 5 O 2735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Conformer: "B" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} bond proxies already assigned to first conformer: 809 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 699 Chain: "E" Number of atoms: 805 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 94, 772 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 94, 772 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} bond proxies already assigned to first conformer: 746 Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 bond proxies already assigned to first conformer: 823 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2865 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "J" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2834 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 54 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG A 54 " occ=0.57 residue: pdb=" N AHIS D 83 " occ=0.56 ... (18 atoms not shown) pdb=" NE2BHIS D 83 " occ=0.44 residue: pdb=" N AARG D 87 " occ=0.56 ... (20 atoms not shown) pdb=" NH2BARG D 87 " occ=0.44 residue: pdb=" N AHIS D 110 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 110 " occ=0.50 residue: pdb=" N AARG E 43 " occ=0.35 ... (20 atoms not shown) pdb=" NH2BARG E 43 " occ=0.65 residue: pdb=" N AARG E 53 " occ=0.47 ... (20 atoms not shown) pdb=" NH2BARG E 53 " occ=0.53 residue: pdb=" N AARG E 64 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG E 64 " occ=0.41 residue: pdb=" N AARG G 100 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG G 100 " occ=0.48 Time building chain proxies: 3.35, per 1000 atoms: 0.28 Number of scatterers: 11785 At special positions: 0 Unit cell: (77.015, 117.105, 135.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 278 15.00 O 2735 8.00 N 2228 7.00 C 6534 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 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 430.2 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 70.9% alpha, 2.6% beta 138 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.119A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.607A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.345A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.576A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.538A pdb=" N ILE D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.525A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.534A pdb=" N PHE E 68 " --> pdb=" O AARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.715A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.512A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.575A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 105 through 125 removed outlier: 3.601A pdb=" N ALA H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.143A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.365A pdb=" N THR B 97 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.424A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.712A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.452A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79 399 hydrogen bonds defined for protein. 1189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.11 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: 2569 1.34 - 1.45: 3860 1.45 - 1.57: 5562 1.57 - 1.69: 554 1.69 - 1.81: 20 Bond restraints: 12565 Sorted by residual: bond pdb=" C3' DA J 112 " pdb=" C2' DA J 112 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C5' DT I 11 " pdb=" C4' DT I 11 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.12e+01 bond pdb=" C3' DG J 39 " pdb=" C2' DG J 39 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG J 29 " pdb=" C2' DG J 29 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DT I 81 " pdb=" C2' DT I 81 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 12560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 17407 1.84 - 3.68: 735 3.68 - 5.52: 21 5.52 - 7.36: 1 7.36 - 9.20: 1 Bond angle restraints: 18165 Sorted by residual: angle pdb=" N3 DT J 38 " pdb=" C4 DT J 38 " pdb=" O4 DT J 38 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT I 36 " pdb=" C4 DT I 36 " pdb=" O4 DT I 36 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 18 " pdb=" C4 DT J 18 " pdb=" O4 DT J 18 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 49 " pdb=" C4 DT I 49 " pdb=" O4 DT I 49 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 91 " pdb=" C4 DT I 91 " pdb=" O4 DT I 91 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 18160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 5460 35.26 - 70.52: 1374 70.52 - 105.79: 24 105.79 - 141.05: 4 141.05 - 176.31: 2 Dihedral angle restraints: 6864 sinusoidal: 4642 harmonic: 2222 Sorted by residual: dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DG J 16 " ideal model delta sinusoidal sigma weight residual -140.00 36.31 -176.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 137 " pdb=" C3' DA J 137 " pdb=" O3' DA J 137 " pdb=" P DA J 138 " ideal model delta sinusoidal sigma weight residual 220.00 48.32 171.68 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 29 " pdb=" C3' DG J 29 " pdb=" O3' DG J 29 " pdb=" P DC J 30 " ideal model delta sinusoidal sigma weight residual 220.00 86.06 133.94 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1398 0.039 - 0.078: 490 0.078 - 0.117: 157 0.117 - 0.156: 15 0.156 - 0.195: 1 Chirality restraints: 2061 Sorted by residual: chirality pdb=" C3' DA J 137 " pdb=" C4' DA J 137 " pdb=" O3' DA J 137 " pdb=" C2' DA J 137 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" C3' DA J 96 " pdb=" C4' DA J 96 " pdb=" O3' DA J 96 " pdb=" C2' DA J 96 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" C3' DT I 114 " pdb=" C4' DT I 114 " pdb=" O3' DT I 114 " pdb=" C2' DT I 114 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2058 not shown) Planarity restraints: 1343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 77 " 0.022 2.00e-02 2.50e+03 9.27e-03 2.58e+00 pdb=" N9 DG I 77 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG I 77 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 77 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 77 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 77 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 77 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 77 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 77 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 77 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 77 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 77 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 63 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C LEU F 63 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU F 63 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU F 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 80 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO C 81 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.021 5.00e-02 4.00e+02 ... (remaining 1340 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1754 2.76 - 3.30: 10427 3.30 - 3.83: 23586 3.83 - 4.37: 27077 4.37 - 4.90: 39784 Nonbonded interactions: 102628 Sorted by model distance: nonbonded pdb=" OD2 ASP D 69 " pdb=" OH TYR F 99 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR B 74 " pdb=" OD2 ASP B 86 " model vdw 2.253 3.040 nonbonded pdb=" NH2 ARG H 87 " pdb=" OP2 DC J 55 " model vdw 2.265 3.120 nonbonded pdb=" NH1 ARG G 82 " pdb=" O VAL G 108 " model vdw 2.267 3.120 nonbonded pdb=" NH2 ARG B 36 " pdb=" OP2 DA J 96 " model vdw 2.299 3.120 ... (remaining 102623 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 42 or resid 44 through 52 or resid 55 through 6 \ 3 or resid 65 through 134)) selection = (chain 'E' and (resid 41 through 42 or resid 44 through 52 or resid 55 through 6 \ 3 or resid 65 through 134)) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = (chain 'C' and (resid 12 through 24 or resid 26 through 99 or resid 101 through \ 118)) selection = (chain 'G' and (resid 12 through 99 or resid 101 through 118)) } ncs_group { reference = (chain 'D' and (resid 33 through 82 or resid 84 through 86 or resid 88 through 1 \ 09 or resid 111 through 125)) selection = (chain 'H' and (resid 33 through 82 or resid 84 through 86 or resid 88 through 1 \ 09 or resid 111 through 125)) } 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=0.35 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.550 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.006 0.041 12565 Z= 0.503 Angle : 0.718 9.202 18165 Z= 0.656 Chirality : 0.043 0.195 2061 Planarity : 0.004 0.037 1343 Dihedral : 28.713 176.311 5436 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.16 % Allowed : 20.00 % Favored : 79.84 % 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 are not related in a simple way. whole: 1.40 (0.31), residues: 763 helix: 1.72 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -1.20 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.010 0.001 TYR G 58 PHE 0.006 0.001 PHE B 62 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.50 (12565) covalent geometry : angle 0.71791 / 0.66 (18165) hydrogen bonds : bond 0.11141 / 6.97 ( 750) hydrogen bonds : angle 4.33436 / 3.18 ( 1891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.302 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1806 time to fit residues: 17.7924 Evaluate side-chains 76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0000 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.169150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107973 restraints weight = 64575.743| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.95 r_work: 0.2837 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12565 Z= 0.157 Angle : 0.618 7.717 18165 Z= 0.368 Chirality : 0.044 0.365 2061 Planarity : 0.004 0.039 1343 Dihedral : 31.427 174.056 3917 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.63 % Allowed : 19.53 % Favored : 79.84 % 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 are not related in a simple way. whole: 1.76 (0.30), residues: 763 helix: 1.92 (0.22), residues: 559 sheet: None (None), residues: 0 loop : -0.95 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 12 TYR 0.010 0.001 TYR G 58 PHE 0.008 0.001 PHE A 68 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (12565) covalent geometry : angle 0.61762 / 0.37 (18165) hydrogen bonds : bond 0.04715 / 3.20 ( 750) hydrogen bonds : angle 2.97137 / 2.09 ( 1891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.239 Fit side-chains REVERT: A 130 ARG cc_start: 0.8593 (tpt-90) cc_final: 0.7570 (tpt90) REVERT: C 74 ASN cc_start: 0.7412 (m-40) cc_final: 0.6772 (t0) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.1464 time to fit residues: 15.3269 Evaluate side-chains 76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105433 restraints weight = 57481.610| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.90 r_work: 0.2835 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12565 Z= 0.164 Angle : 0.608 7.823 18165 Z= 0.359 Chirality : 0.043 0.344 2061 Planarity : 0.004 0.039 1343 Dihedral : 31.699 174.428 3913 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.57 % Allowed : 18.74 % Favored : 79.69 % 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 are not related in a simple way. whole: 1.86 (0.30), residues: 763 helix: 1.99 (0.22), residues: 561 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 72 TYR 0.011 0.001 TYR G 58 PHE 0.008 0.001 PHE E 68 HIS 0.005 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (12565) covalent geometry : angle 0.60835 / 0.36 (18165) hydrogen bonds : bond 0.04473 / 3.08 ( 750) hydrogen bonds : angle 2.77775 / 1.95 ( 1891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.301 Fit side-chains REVERT: C 74 ASN cc_start: 0.7139 (m-40) cc_final: 0.6501 (t0) outliers start: 10 outliers final: 3 residues processed: 83 average time/residue: 0.1385 time to fit residues: 15.4096 Evaluate side-chains 77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.168769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107506 restraints weight = 61875.397| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.10 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12565 Z= 0.146 Angle : 0.600 8.426 18165 Z= 0.352 Chirality : 0.043 0.345 2061 Planarity : 0.004 0.040 1343 Dihedral : 31.706 174.142 3913 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.26 % Allowed : 19.37 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.30), residues: 763 helix: 2.06 (0.22), residues: 561 sheet: None (None), residues: 0 loop : -0.88 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 72 TYR 0.010 0.001 TYR G 58 PHE 0.007 0.001 PHE A 68 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (12565) covalent geometry : angle 0.60031 / 0.35 (18165) hydrogen bonds : bond 0.04202 / 2.90 ( 750) hydrogen bonds : angle 2.72204 / 1.91 ( 1891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.199 Fit side-chains REVERT: A 91 MET cc_start: 0.7669 (tpp) cc_final: 0.7242 (mmt) REVERT: C 74 ASN cc_start: 0.7179 (m-40) cc_final: 0.6530 (t0) REVERT: D 63 MET cc_start: 0.8213 (mmm) cc_final: 0.7999 (mmp) outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.1275 time to fit residues: 13.8201 Evaluate side-chains 79 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.167415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104101 restraints weight = 56251.099| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.84 r_work: 0.2831 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12565 Z= 0.177 Angle : 0.624 8.324 18165 Z= 0.360 Chirality : 0.044 0.334 2061 Planarity : 0.004 0.039 1343 Dihedral : 31.842 173.964 3913 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.73 % Allowed : 19.53 % Favored : 78.74 % 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 are not related in a simple way. whole: 1.86 (0.30), residues: 763 helix: 1.99 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.011 0.001 TYR G 58 PHE 0.008 0.001 PHE E 68 HIS 0.005 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (12565) covalent geometry : angle 0.62421 / 0.36 (18165) hydrogen bonds : bond 0.04391 / 3.05 ( 750) hydrogen bonds : angle 2.75471 / 1.93 ( 1891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.310 Fit side-chains REVERT: C 74 ASN cc_start: 0.7214 (m-40) cc_final: 0.6524 (t0) REVERT: F 51 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8539 (pt) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.1392 time to fit residues: 14.4214 Evaluate side-chains 77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104654 restraints weight = 59478.779| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.89 r_work: 0.2823 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12565 Z= 0.179 Angle : 0.621 8.313 18165 Z= 0.358 Chirality : 0.044 0.331 2061 Planarity : 0.004 0.039 1343 Dihedral : 31.886 173.784 3913 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.57 % Allowed : 19.69 % Favored : 78.74 % 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 are not related in a simple way. whole: 1.87 (0.30), residues: 763 helix: 1.98 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -0.90 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 72 TYR 0.010 0.001 TYR H 38 PHE 0.008 0.001 PHE A 68 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (12565) covalent geometry : angle 0.62122 / 0.36 (18165) hydrogen bonds : bond 0.04308 / 2.99 ( 750) hydrogen bonds : angle 2.74539 / 1.93 ( 1891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.287 Fit side-chains REVERT: C 74 ASN cc_start: 0.7239 (m-40) cc_final: 0.6544 (t0) REVERT: F 51 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8554 (pt) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 0.1358 time to fit residues: 13.9397 Evaluate side-chains 78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104767 restraints weight = 52371.977| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.75 r_work: 0.2836 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12565 Z= 0.158 Angle : 0.612 8.338 18165 Z= 0.354 Chirality : 0.043 0.323 2061 Planarity : 0.004 0.039 1343 Dihedral : 31.874 173.652 3913 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 19.53 % Favored : 78.58 % 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 are not related in a simple way. whole: 1.97 (0.30), residues: 763 helix: 2.03 (0.22), residues: 561 sheet: None (None), residues: 0 loop : -0.80 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 72 TYR 0.010 0.001 TYR H 38 PHE 0.007 0.001 PHE A 68 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12565) covalent geometry : angle 0.61179 / 0.35 (18165) hydrogen bonds : bond 0.04154 / 2.89 ( 750) hydrogen bonds : angle 2.70299 / 1.90 ( 1891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.255 Fit side-chains REVERT: A 130 ARG cc_start: 0.8535 (tpt-90) cc_final: 0.7182 (tpt90) REVERT: C 74 ASN cc_start: 0.7224 (m-40) cc_final: 0.6535 (t0) REVERT: F 51 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8506 (pt) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.1520 time to fit residues: 15.9835 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125793 restraints weight = 57785.092| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.25 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12565 Z= 0.262 Angle : 0.688 8.086 18165 Z= 0.384 Chirality : 0.048 0.332 2061 Planarity : 0.005 0.041 1343 Dihedral : 32.156 173.289 3913 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.20 % Allowed : 18.90 % Favored : 78.90 % 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 are not related in a simple way. whole: 1.47 (0.30), residues: 763 helix: 1.69 (0.22), residues: 560 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 72 TYR 0.014 0.002 TYR H 43 PHE 0.011 0.002 PHE E 68 HIS 0.005 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.26 (12565) covalent geometry : angle 0.68753 / 0.38 (18165) hydrogen bonds : bond 0.04946 / 3.44 ( 750) hydrogen bonds : angle 2.92274 / 2.06 ( 1891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.298 Fit side-chains REVERT: C 74 ASN cc_start: 0.7657 (m-40) cc_final: 0.7202 (t0) REVERT: F 51 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8449 (pt) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 0.1524 time to fit residues: 16.4458 Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124110 restraints weight = 56027.125| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.72 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12565 Z= 0.151 Angle : 0.615 8.325 18165 Z= 0.355 Chirality : 0.043 0.311 2061 Planarity : 0.004 0.039 1343 Dihedral : 32.002 173.255 3913 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.57 % Allowed : 19.69 % Favored : 78.74 % 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 are not related in a simple way. whole: 1.84 (0.30), residues: 763 helix: 1.93 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -0.82 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 72 TYR 0.010 0.001 TYR H 38 PHE 0.007 0.001 PHE B 62 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12565) covalent geometry : angle 0.61548 / 0.36 (18165) hydrogen bonds : bond 0.04086 / 2.84 ( 750) hydrogen bonds : angle 2.71911 / 1.91 ( 1891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.206 Fit side-chains REVERT: C 74 ASN cc_start: 0.7535 (m-40) cc_final: 0.6916 (t0) REVERT: F 51 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8271 (pt) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.1344 time to fit residues: 14.0616 Evaluate side-chains 78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133207 restraints weight = 51188.267| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.35 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.003 0.043 12565 Z= 0.143 Angle : 0.606 10.794 18165 Z= 0.351 Chirality : 0.042 0.306 2061 Planarity : 0.004 0.040 1343 Dihedral : 31.930 172.717 3913 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.10 % Allowed : 20.00 % Favored : 78.90 % 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 are not related in a simple way. whole: 2.06 (0.30), residues: 763 helix: 2.08 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.72 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.010 0.001 TYR G 58 PHE 0.006 0.001 PHE E 68 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (12565) covalent geometry : angle 0.60578 / 0.35 (18165) hydrogen bonds : bond 0.03945 / 2.76 ( 750) hydrogen bonds : angle 2.64264 / 1.85 ( 1891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.205 Fit side-chains REVERT: A 91 MET cc_start: 0.7440 (tpp) cc_final: 0.7084 (mmt) REVERT: A 130 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7496 (tpt90) REVERT: C 74 ASN cc_start: 0.7706 (m-40) cc_final: 0.7167 (t0) REVERT: F 51 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8427 (pt) REVERT: H 60 MET cc_start: 0.8071 (tpp) cc_final: 0.7832 (mmm) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.1314 time to fit residues: 13.1300 Evaluate side-chains 74 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129737 restraints weight = 45983.100| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.08 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12565 Z= 0.215 Angle : 0.648 8.387 18165 Z= 0.367 Chirality : 0.045 0.311 2061 Planarity : 0.005 0.041 1343 Dihedral : 32.071 172.630 3913 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.42 % Allowed : 19.84 % Favored : 78.74 % 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 are not related in a simple way. whole: 1.79 (0.30), residues: 763 helix: 1.89 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -0.82 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.011 0.002 TYR H 38 PHE 0.009 0.002 PHE E 68 HIS 0.004 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (12565) covalent geometry : angle 0.64772 / 0.37 (18165) hydrogen bonds : bond 0.04439 / 3.10 ( 750) hydrogen bonds : angle 2.77947 / 1.96 ( 1891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.30 seconds wall clock time: 37 minutes 36.64 seconds (2256.64 seconds total)