Starting phenix.real_space_refine on Fri Jul 3 17:55:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8m_61231/07_2026/9j8m_61231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8m_61231/07_2026/9j8m_61231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8m_61231/07_2026/9j8m_61231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8m_61231/07_2026/9j8m_61231.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8m_61231/07_2026/9j8m_61231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8m_61231/07_2026/9j8m_61231.cif" } resolution = 3.82 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: 5 Type Number sf(0) Gaussians P 368 5.49 5 S 27 5.16 5 C 8796 2.51 5 N 2945 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15831 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3753 Classifications: {'DNA': 184} Link IDs: {'rna3p': 183} Chain: "J" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3791 Classifications: {'DNA': 184} Link IDs: {'rna3p': 183} Chain: "K" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "L" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG M 453 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG M 453 " occ=0.50 Time building chain proxies: 2.88, per 1000 atoms: 0.18 Number of scatterers: 15831 At special positions: 0 Unit cell: (167.48, 117.66, 145.22, 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 27 16.00 P 368 15.00 O 3695 8.00 N 2945 7.00 C 8796 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: 0.94 Conformation dependent library (CDL) restraints added in 414.0 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 66.7% alpha, 6.9% beta 184 base pairs and 311 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.531A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.686A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.581A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.501A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.504A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.620A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.569A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.009A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.911A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.605A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.728A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 4 through 13 removed outlier: 3.950A pdb=" N GLU K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 41 through 52 Processing helix chain 'K' and resid 55 through 68 Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'L' and resid 4 through 13 removed outlier: 4.030A pdb=" N GLU L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 38 Processing helix chain 'L' and resid 41 through 52 Processing helix chain 'L' and resid 55 through 68 Processing helix chain 'L' and resid 70 through 89 Processing helix chain 'M' and resid 501 through 503 No H-bonds generated for 'chain 'M' and resid 501 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.558A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.373A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.384A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.349A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 8.000A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 430 through 436 removed outlier: 3.530A pdb=" N ALA M 539 " --> pdb=" O LEU M 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 440 through 445 removed outlier: 5.520A pdb=" N VAL M 442 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG M 455 " --> pdb=" O VAL M 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 462 through 463 529 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 473 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 311 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3182 1.33 - 1.45: 5359 1.45 - 1.57: 7558 1.57 - 1.69: 734 1.69 - 1.81: 41 Bond restraints: 16874 Sorted by residual: bond pdb=" C3' DG I 29 " pdb=" C2' DG I 29 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DT J 82 " pdb=" C2' DT J 82 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC I 25 " pdb=" C2' DC I 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DG I 56 " pdb=" C2' DG I 56 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I 96 " pdb=" C2' DC I 96 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 16869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 22491 1.30 - 2.59: 1733 2.59 - 3.89: 128 3.89 - 5.18: 8 5.18 - 6.48: 3 Bond angle restraints: 24363 Sorted by residual: angle pdb=" O4' DG J 80 " pdb=" C4' DG J 80 " pdb=" C3' DG J 80 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.34e+01 angle pdb=" O4' DA I 113 " pdb=" C4' DA I 113 " pdb=" C3' DA I 113 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT J 82 " pdb=" C4 DT J 82 " pdb=" O4 DT J 82 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 186 " pdb=" C4 DT I 186 " pdb=" O4 DT I 186 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 24358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 7534 35.45 - 70.90: 1601 70.90 - 106.35: 17 106.35 - 141.80: 0 141.80 - 177.25: 2 Dihedral angle restraints: 9154 sinusoidal: 6151 harmonic: 3003 Sorted by residual: dihedral pdb=" C4' DT J 152 " pdb=" C3' DT J 152 " pdb=" O3' DT J 152 " pdb=" P DC J 153 " ideal model delta sinusoidal sigma weight residual 220.00 42.75 177.25 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 118 " pdb=" C3' DG J 118 " pdb=" O3' DG J 118 " pdb=" P DG J 119 " ideal model delta sinusoidal sigma weight residual 220.00 75.54 144.46 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" N LEU A 65 " pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " pdb=" CG LEU A 65 " ideal model delta sinusoidal sigma weight residual -60.00 -118.92 58.92 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 9151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1378 0.028 - 0.057: 922 0.057 - 0.085: 282 0.085 - 0.113: 143 0.113 - 0.142: 17 Chirality restraints: 2742 Sorted by residual: chirality pdb=" P DG J 100 " pdb=" OP1 DG J 100 " pdb=" OP2 DG J 100 " pdb=" O5' DG J 100 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" C3' DT J 152 " pdb=" C4' DT J 152 " pdb=" O3' DT J 152 " pdb=" C2' DT J 152 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ASN M 466 " pdb=" N ASN M 466 " pdb=" C ASN M 466 " pdb=" CB ASN M 466 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2739 not shown) Planarity restraints: 1819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 113 " -0.024 2.00e-02 2.50e+03 1.06e-02 3.08e+00 pdb=" N9 DA I 113 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 113 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 113 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 113 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 113 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 113 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 113 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 113 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 113 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 113 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 42 " -0.021 2.00e-02 2.50e+03 9.50e-03 2.48e+00 pdb=" N9 DA I 42 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 42 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 42 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 42 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 42 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 42 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 42 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 42 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 42 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 42 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 41 " -0.019 2.00e-02 2.50e+03 8.18e-03 2.01e+00 pdb=" N9 DG I 41 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 41 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 41 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 41 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 41 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 41 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 41 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 41 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 41 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 41 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 41 " -0.001 2.00e-02 2.50e+03 ... (remaining 1816 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2979 2.79 - 3.32: 14177 3.32 - 3.85: 30836 3.85 - 4.37: 34903 4.37 - 4.90: 50618 Nonbonded interactions: 133513 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.264 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.282 3.040 nonbonded pdb=" NH2 ARG G 20 " pdb=" OP1 DT I 54 " model vdw 2.317 3.120 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.328 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.328 3.040 ... (remaining 133508 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' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.005 0.046 16874 Z= 0.503 Angle : 0.688 6.479 24363 Z= 0.630 Chirality : 0.042 0.142 2742 Planarity : 0.003 0.031 1819 Dihedral : 26.318 177.245 7220 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.49 % Allowed : 3.79 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 3.02 (0.26), residues: 1025 helix: 2.81 (0.20), residues: 657 sheet: 2.21 (0.79), residues: 50 loop : 0.22 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.012 0.001 TYR G 57 PHE 0.006 0.001 PHE L 49 TRP 0.006 0.001 TRP M 498 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.50 (16874) covalent geometry : angle 0.68826 / 0.63 (24363) hydrogen bonds : bond 0.10776 / 7.39 ( 1002) hydrogen bonds : angle 4.22333 / 3.19 ( 2493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 TYR cc_start: 0.7640 (t80) cc_final: 0.7381 (t80) REVERT: L 6 LYS cc_start: 0.6747 (tttm) cc_final: 0.6040 (mtmm) outliers start: 13 outliers final: 6 residues processed: 218 average time/residue: 0.1680 time to fit residues: 49.5918 Evaluate side-chains 101 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain L residue 80 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN D 49 HIS E 39 HIS E 108 ASN F 75 HIS F 93 GLN G 112 GLN H 95 GLN L 5 GLN L 7 HIS L 48 GLN ** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 517 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.053398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.036531 restraints weight = 127167.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.037344 restraints weight = 62064.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.037840 restraints weight = 40776.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038117 restraints weight = 32480.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.038172 restraints weight = 28908.466| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16874 Z= 0.240 Angle : 0.675 7.634 24363 Z= 0.398 Chirality : 0.043 0.223 2742 Planarity : 0.005 0.053 1819 Dihedral : 30.277 176.866 5176 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.64 % Allowed : 10.45 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.66 (0.26), residues: 1025 helix: 2.52 (0.20), residues: 665 sheet: 1.52 (0.77), residues: 50 loop : 0.15 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 482 TYR 0.024 0.002 TYR F 88 PHE 0.026 0.002 PHE L 59 TRP 0.019 0.003 TRP L 84 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 (16874) covalent geometry : angle 0.67546 / 0.40 (24363) hydrogen bonds : bond 0.05866 / 4.03 ( 1002) hydrogen bonds : angle 3.83474 / 2.85 ( 2493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLU cc_start: 0.8715 (mp0) cc_final: 0.8513 (mp0) REVERT: H 42 TYR cc_start: 0.8070 (t80) cc_final: 0.7830 (t80) REVERT: K 82 ARG cc_start: 0.8906 (tmm-80) cc_final: 0.8380 (tpm170) REVERT: L 6 LYS cc_start: 0.8651 (tttm) cc_final: 0.7746 (pttm) REVERT: M 447 GLU cc_start: 0.8425 (mp0) cc_final: 0.7761 (mt-10) REVERT: M 481 TYR cc_start: 0.8088 (t80) cc_final: 0.7868 (t80) outliers start: 23 outliers final: 12 residues processed: 119 average time/residue: 0.1179 time to fit residues: 20.9270 Evaluate side-chains 97 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 87 optimal weight: 50.0000 chunk 120 optimal weight: 8.9990 chunk 74 optimal weight: 40.0000 chunk 113 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 109 HIS E 108 ASN M 468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.054081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038206 restraints weight = 127460.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.038958 restraints weight = 64793.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.039403 restraints weight = 43333.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.039673 restraints weight = 34913.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039807 restraints weight = 31302.121| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16874 Z= 0.237 Angle : 0.661 9.158 24363 Z= 0.388 Chirality : 0.042 0.221 2742 Planarity : 0.005 0.055 1819 Dihedral : 30.581 177.412 5172 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.21 % Allowed : 12.17 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.32 (0.26), residues: 1025 helix: 2.27 (0.20), residues: 670 sheet: 1.12 (0.81), residues: 50 loop : -0.02 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 75 TYR 0.018 0.002 TYR B 88 PHE 0.028 0.002 PHE K 59 TRP 0.015 0.002 TRP M 498 HIS 0.005 0.002 HIS L 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.24 (16874) covalent geometry : angle 0.66110 / 0.39 (24363) hydrogen bonds : bond 0.05940 / 4.08 ( 1002) hydrogen bonds : angle 3.70184 / 2.74 ( 2493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.9017 (t0) REVERT: C 91 GLU cc_start: 0.8371 (tp30) cc_final: 0.8136 (tp30) REVERT: D 51 ASP cc_start: 0.8512 (p0) cc_final: 0.8312 (p0) REVERT: H 42 TYR cc_start: 0.8014 (t80) cc_final: 0.7767 (t80) REVERT: K 10 PHE cc_start: 0.7511 (t80) cc_final: 0.7268 (t80) REVERT: K 15 MET cc_start: 0.6859 (pmm) cc_final: 0.6560 (pmm) REVERT: K 82 ARG cc_start: 0.8947 (tmm-80) cc_final: 0.8312 (tpm170) REVERT: L 6 LYS cc_start: 0.8748 (tttm) cc_final: 0.8020 (pttm) REVERT: M 470 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8069 (mmtm) REVERT: M 481 TYR cc_start: 0.7944 (t80) cc_final: 0.7672 (t80) outliers start: 28 outliers final: 14 residues processed: 119 average time/residue: 0.1115 time to fit residues: 19.8131 Evaluate side-chains 103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 85 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 91 optimal weight: 50.0000 chunk 100 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 0.1980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.053224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036659 restraints weight = 126330.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037469 restraints weight = 59964.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.037962 restraints weight = 39154.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038245 restraints weight = 31172.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.038350 restraints weight = 27808.095| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16874 Z= 0.147 Angle : 0.590 7.670 24363 Z= 0.357 Chirality : 0.041 0.214 2742 Planarity : 0.004 0.044 1819 Dihedral : 30.524 176.700 5172 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.95 % Allowed : 13.43 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.63 (0.26), residues: 1025 helix: 2.53 (0.20), residues: 668 sheet: 1.30 (0.83), residues: 50 loop : 0.06 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 82 TYR 0.020 0.001 TYR K 43 PHE 0.027 0.002 PHE L 59 TRP 0.013 0.001 TRP M 498 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (16874) covalent geometry : angle 0.59029 / 0.36 (24363) hydrogen bonds : bond 0.04775 / 3.28 ( 1002) hydrogen bonds : angle 3.38581 / 2.50 ( 2493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8529 (tp30) cc_final: 0.8201 (tp30) REVERT: D 51 ASP cc_start: 0.8783 (p0) cc_final: 0.8573 (p0) REVERT: E 97 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7090 (mt-10) REVERT: H 42 TYR cc_start: 0.7924 (t80) cc_final: 0.7693 (t80) REVERT: K 10 PHE cc_start: 0.7455 (t80) cc_final: 0.7218 (t80) REVERT: L 6 LYS cc_start: 0.8751 (tttm) cc_final: 0.8060 (pttm) REVERT: M 447 GLU cc_start: 0.8451 (mp0) cc_final: 0.7678 (mt-10) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 0.1134 time to fit residues: 18.6293 Evaluate side-chains 101 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 11 optimal weight: 0.7980 chunk 89 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 2 optimal weight: 0.3980 chunk 61 optimal weight: 0.4980 chunk 60 optimal weight: 0.0980 chunk 115 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.053955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037286 restraints weight = 126439.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038049 restraints weight = 59830.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.038565 restraints weight = 38741.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.038835 restraints weight = 30712.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.039011 restraints weight = 27356.138| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16874 Z= 0.132 Angle : 0.568 8.476 24363 Z= 0.346 Chirality : 0.040 0.212 2742 Planarity : 0.004 0.039 1819 Dihedral : 30.387 176.305 5172 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.95 % Allowed : 14.35 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.81 (0.27), residues: 1025 helix: 2.69 (0.20), residues: 668 sheet: 1.15 (0.83), residues: 50 loop : 0.12 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 82 TYR 0.019 0.002 TYR B 51 PHE 0.025 0.002 PHE K 59 TRP 0.018 0.002 TRP M 514 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.13 (16874) covalent geometry : angle 0.56789 / 0.35 (24363) hydrogen bonds : bond 0.04159 / 2.87 ( 1002) hydrogen bonds : angle 3.21593 / 2.36 ( 2493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8488 (tp30) cc_final: 0.8169 (tp30) REVERT: E 97 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7083 (mt-10) REVERT: F 84 MET cc_start: 0.8280 (mmm) cc_final: 0.8076 (mmm) REVERT: F 88 TYR cc_start: 0.8939 (m-10) cc_final: 0.8722 (m-10) REVERT: H 42 TYR cc_start: 0.7799 (t80) cc_final: 0.7523 (t80) REVERT: K 10 PHE cc_start: 0.7320 (t80) cc_final: 0.7065 (t80) REVERT: K 13 GLU cc_start: 0.9147 (pm20) cc_final: 0.8784 (pm20) REVERT: K 56 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8703 (tm-30) REVERT: K 61 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7700 (mp0) REVERT: K 82 ARG cc_start: 0.8995 (tmm-80) cc_final: 0.8759 (mmt180) REVERT: L 6 LYS cc_start: 0.8744 (tttm) cc_final: 0.8023 (ptpp) outliers start: 17 outliers final: 14 residues processed: 116 average time/residue: 0.1214 time to fit residues: 20.8214 Evaluate side-chains 106 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 104 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 40.0000 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.053936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.038092 restraints weight = 127811.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.038803 restraints weight = 66916.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.039256 restraints weight = 45550.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.039488 restraints weight = 37129.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.039588 restraints weight = 33426.381| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16874 Z= 0.265 Angle : 0.684 8.963 24363 Z= 0.393 Chirality : 0.042 0.217 2742 Planarity : 0.005 0.045 1819 Dihedral : 30.587 176.745 5168 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.76 % Allowed : 15.04 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.43 (0.26), residues: 1025 helix: 2.33 (0.19), residues: 671 sheet: 1.18 (0.84), residues: 49 loop : 0.07 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 37 TYR 0.015 0.002 TYR A 99 PHE 0.026 0.002 PHE L 59 TRP 0.013 0.002 TRP M 498 HIS 0.006 0.002 HIS L 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.27 (16874) covalent geometry : angle 0.68402 / 0.39 (24363) hydrogen bonds : bond 0.06157 / 4.22 ( 1002) hydrogen bonds : angle 3.63865 / 2.71 ( 2493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 TYR cc_start: 0.8073 (t80) cc_final: 0.7822 (t80) REVERT: K 10 PHE cc_start: 0.7370 (t80) cc_final: 0.7081 (t80) REVERT: K 56 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8825 (tm-30) REVERT: K 82 ARG cc_start: 0.8986 (tmm-80) cc_final: 0.8744 (mmt180) REVERT: L 6 LYS cc_start: 0.8843 (tttm) cc_final: 0.8101 (ptpp) REVERT: M 447 GLU cc_start: 0.8244 (mp0) cc_final: 0.7631 (mt-10) outliers start: 24 outliers final: 22 residues processed: 104 average time/residue: 0.1169 time to fit residues: 18.2950 Evaluate side-chains 107 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain M residue 433 HIS Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 132 optimal weight: 30.0000 chunk 130 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 96 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.054121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.038295 restraints weight = 125714.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.039019 restraints weight = 66497.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.039446 restraints weight = 45662.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.039718 restraints weight = 37258.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.039834 restraints weight = 33556.094| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16874 Z= 0.190 Angle : 0.613 7.064 24363 Z= 0.363 Chirality : 0.040 0.215 2742 Planarity : 0.004 0.060 1819 Dihedral : 30.617 176.405 5168 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 16.99 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.55 (0.26), residues: 1025 helix: 2.47 (0.20), residues: 670 sheet: 1.11 (0.83), residues: 49 loop : 0.03 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 60 TYR 0.013 0.002 TYR G 57 PHE 0.021 0.002 PHE L 49 TRP 0.011 0.001 TRP M 498 HIS 0.005 0.001 HIS L 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (16874) covalent geometry : angle 0.61305 / 0.36 (24363) hydrogen bonds : bond 0.05050 / 3.48 ( 1002) hydrogen bonds : angle 3.43733 / 2.56 ( 2493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8646 (mmm) cc_final: 0.8378 (mmm) REVERT: H 42 TYR cc_start: 0.7894 (t80) cc_final: 0.7584 (t80) REVERT: K 56 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8701 (tm-30) REVERT: K 82 ARG cc_start: 0.9002 (tmm-80) cc_final: 0.8762 (mmt180) REVERT: L 6 LYS cc_start: 0.8880 (tttm) cc_final: 0.8140 (ptpp) outliers start: 18 outliers final: 16 residues processed: 105 average time/residue: 0.1186 time to fit residues: 18.4383 Evaluate side-chains 106 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.052790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.036350 restraints weight = 127328.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037159 restraints weight = 61298.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.037638 restraints weight = 40288.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037899 restraints weight = 32158.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038022 restraints weight = 28665.270| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16874 Z= 0.172 Angle : 0.604 8.104 24363 Z= 0.359 Chirality : 0.040 0.213 2742 Planarity : 0.004 0.037 1819 Dihedral : 30.582 176.332 5168 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.18 % Allowed : 16.53 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.61 (0.26), residues: 1025 helix: 2.55 (0.20), residues: 670 sheet: 0.95 (0.83), residues: 49 loop : 0.00 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 60 TYR 0.013 0.001 TYR G 57 PHE 0.022 0.002 PHE L 59 TRP 0.010 0.001 TRP M 498 HIS 0.006 0.001 HIS L 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (16874) covalent geometry : angle 0.60394 / 0.36 (24363) hydrogen bonds : bond 0.04832 / 3.33 ( 1002) hydrogen bonds : angle 3.34167 / 2.48 ( 2493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 TYR cc_start: 0.7989 (t80) cc_final: 0.7698 (t80) REVERT: K 56 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8519 (tm-30) REVERT: K 57 ASP cc_start: 0.9252 (t70) cc_final: 0.9000 (t70) REVERT: K 60 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7127 (tmt-80) REVERT: K 61 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8472 (mp0) REVERT: K 82 ARG cc_start: 0.9017 (tmm-80) cc_final: 0.8771 (mmt180) REVERT: L 6 LYS cc_start: 0.8854 (tttm) cc_final: 0.8229 (ptpp) REVERT: M 447 GLU cc_start: 0.8498 (mp0) cc_final: 0.7703 (mt-10) outliers start: 19 outliers final: 17 residues processed: 106 average time/residue: 0.1187 time to fit residues: 18.4527 Evaluate side-chains 108 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 91 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 chunk 102 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.052662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036019 restraints weight = 126952.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036810 restraints weight = 62490.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.037275 restraints weight = 41403.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037545 restraints weight = 33279.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.037672 restraints weight = 29716.771| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16874 Z= 0.183 Angle : 0.627 11.230 24363 Z= 0.366 Chirality : 0.040 0.211 2742 Planarity : 0.004 0.039 1819 Dihedral : 30.615 176.014 5167 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.64 % Allowed : 16.42 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.54 (0.26), residues: 1025 helix: 2.52 (0.20), residues: 669 sheet: 0.98 (0.84), residues: 49 loop : -0.06 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 60 TYR 0.013 0.002 TYR G 57 PHE 0.022 0.002 PHE L 59 TRP 0.012 0.002 TRP K 84 HIS 0.006 0.001 HIS L 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (16874) covalent geometry : angle 0.62724 / 0.37 (24363) hydrogen bonds : bond 0.05010 / 3.45 ( 1002) hydrogen bonds : angle 3.36978 / 2.50 ( 2493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8668 (mmm) cc_final: 0.8293 (mmm) REVERT: H 42 TYR cc_start: 0.8012 (t80) cc_final: 0.7721 (t80) REVERT: K 56 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8556 (tm-30) REVERT: K 60 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7452 (tmt-80) REVERT: K 82 ARG cc_start: 0.8989 (tmm-80) cc_final: 0.8776 (mmt180) REVERT: L 6 LYS cc_start: 0.8853 (tttm) cc_final: 0.8302 (ptpp) REVERT: M 447 GLU cc_start: 0.8323 (mp0) cc_final: 0.7674 (mt-10) outliers start: 23 outliers final: 21 residues processed: 107 average time/residue: 0.1236 time to fit residues: 19.7889 Evaluate side-chains 112 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 49 PHE Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 464 MET Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 chunk 97 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.053064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036496 restraints weight = 127097.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037301 restraints weight = 61517.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037803 restraints weight = 40626.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.038044 restraints weight = 32340.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.038219 restraints weight = 29012.762| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16874 Z= 0.147 Angle : 0.601 9.019 24363 Z= 0.357 Chirality : 0.040 0.208 2742 Planarity : 0.004 0.037 1819 Dihedral : 30.550 175.799 5167 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 17.11 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 2.77 (0.27), residues: 1025 helix: 2.70 (0.20), residues: 670 sheet: 1.23 (0.86), residues: 47 loop : -0.03 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 83 TYR 0.012 0.001 TYR G 57 PHE 0.021 0.001 PHE L 59 TRP 0.013 0.001 TRP K 84 HIS 0.006 0.001 HIS L 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (16874) covalent geometry : angle 0.60087 / 0.36 (24363) hydrogen bonds : bond 0.04380 / 3.03 ( 1002) hydrogen bonds : angle 3.24191 / 2.39 ( 2493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8635 (mmm) cc_final: 0.8298 (mmm) REVERT: H 42 TYR cc_start: 0.7926 (t80) cc_final: 0.7694 (t80) REVERT: K 56 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8542 (tm-30) REVERT: K 57 ASP cc_start: 0.9250 (t70) cc_final: 0.9010 (t70) REVERT: K 60 ARG cc_start: 0.8113 (ptm160) cc_final: 0.7406 (tmt-80) REVERT: K 61 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8462 (mp0) REVERT: L 6 LYS cc_start: 0.8816 (tttm) cc_final: 0.8280 (ptpp) REVERT: M 447 GLU cc_start: 0.8457 (mp0) cc_final: 0.7828 (mt-10) outliers start: 17 outliers final: 17 residues processed: 102 average time/residue: 0.1227 time to fit residues: 18.7432 Evaluate side-chains 105 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 81 optimal weight: 30.0000 chunk 87 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.052661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037941 restraints weight = 126781.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.038018 restraints weight = 75757.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038298 restraints weight = 50607.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.038368 restraints weight = 45812.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.038374 restraints weight = 41846.105| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 16874 Z= 0.376 Angle : 0.800 8.991 24363 Z= 0.445 Chirality : 0.046 0.218 2742 Planarity : 0.006 0.055 1819 Dihedral : 30.898 176.259 5167 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.76 % Allowed : 16.42 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % 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: 1.74 (0.26), residues: 1025 helix: 1.84 (0.19), residues: 669 sheet: 1.08 (0.86), residues: 47 loop : -0.31 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 95 TYR 0.022 0.003 TYR B 51 PHE 0.023 0.003 PHE L 59 TRP 0.014 0.002 TRP M 498 HIS 0.008 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.38 (16874) covalent geometry : angle 0.80034 / 0.45 (24363) hydrogen bonds : bond 0.08024 / 5.48 ( 1002) hydrogen bonds : angle 3.99060 / 2.95 ( 2493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.90 seconds wall clock time: 45 minutes 32.28 seconds (2732.28 seconds total)