Starting phenix.real_space_refine on Thu Sep 18 08:34:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8m_61231/09_2025/9j8m_61231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8m_61231/09_2025/9j8m_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_61231/09_2025/9j8m_61231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8m_61231/09_2025/9j8m_61231.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8m_61231/09_2025/9j8m_61231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8m_61231/09_2025/9j8m_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-2.0-5805/lib/python3.9/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: 3.49, per 1000 atoms: 0.22 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: 1.35 Conformation dependent library (CDL) restraints added in 436.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.79 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: 3.34 Time building geometry restraints manager: 1.83 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=" O3' DG J 102 " pdb=" P DT J 103 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.50e-02 4.44e+03 9.37e+00 bond pdb=" N ASN M 466 " pdb=" CA ASN M 466 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.39e-02 5.18e+03 5.47e+00 bond pdb=" O3' DC J 99 " pdb=" P DG J 100 " ideal model delta sigma weight residual 1.607 1.640 -0.033 1.50e-02 4.44e+03 4.71e+00 bond pdb=" C3' DT J 152 " pdb=" O3' DT J 152 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.32e+00 ... (remaining 16869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 23533 1.30 - 2.59: 782 2.59 - 3.89: 38 3.89 - 5.18: 7 5.18 - 6.48: 3 Bond angle restraints: 24363 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.43 109.23 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 110.77 117.25 -6.48 1.93e+00 2.68e-01 1.13e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 116.79 -5.77 1.86e+00 2.89e-01 9.63e+00 angle pdb=" N LYS G 74 " pdb=" CA LYS G 74 " pdb=" CB LYS G 74 " ideal model delta sigma weight residual 113.65 110.10 3.55 1.47e+00 4.63e-01 5.84e+00 angle pdb=" CA ASN M 466 " pdb=" C ASN M 466 " pdb=" O ASN M 466 " ideal model delta sigma weight residual 120.32 117.72 2.60 1.18e+00 7.18e-01 4.87e+00 ... (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 - 0.026: 1722 0.026 - 0.053: 777 0.053 - 0.079: 165 0.079 - 0.105: 57 0.105 - 0.131: 21 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 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.32e-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 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.450 Find NCS groups from input model: 0.140 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16874 Z= 0.149 Angle : 0.521 6.479 24363 Z= 0.328 Chirality : 0.032 0.131 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 aren 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 covalent geometry : bond 0.00294 (16874) covalent geometry : angle 0.52122 (24363) hydrogen bonds : bond 0.10776 ( 1002) hydrogen bonds : angle 4.22333 ( 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 : 0.462 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: 0.1919 time to fit residues: 56.1475 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 : 0.434 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS E 39 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 93 GLN G 112 GLN H 95 GLN L 5 GLN L 7 HIS ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 GLN M 517 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.053711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037936 restraints weight = 127109.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.038637 restraints weight = 67751.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.039062 restraints weight = 46650.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.039299 restraints weight = 38130.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.039391 restraints weight = 34450.547| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16874 Z= 0.325 Angle : 0.677 7.074 24363 Z= 0.392 Chirality : 0.038 0.163 2742 Planarity : 0.005 0.049 1819 Dihedral : 30.271 179.716 5176 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.53 % Allowed : 11.48 % Favored : 85.99 % 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 aren not related in a simple way. whole: 2.39 (0.26), residues: 1025 helix: 2.29 (0.20), residues: 670 sheet: 1.42 (0.79), residues: 49 loop : 0.06 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 82 TYR 0.023 0.003 TYR F 88 PHE 0.023 0.002 PHE L 59 TRP 0.019 0.003 TRP M 498 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00724 (16874) covalent geometry : angle 0.67730 (24363) hydrogen bonds : bond 0.06604 ( 1002) hydrogen bonds : angle 3.87830 ( 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: 22 poor density : 107 time to evaluate : 0.440 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: 0.8424 (tp30) cc_final: 0.8125 (tp30) REVERT: H 42 TYR cc_start: 0.8063 (t80) cc_final: 0.7805 (t80) REVERT: K 10 PHE cc_start: 0.7098 (t80) cc_final: 0.6694 (t80) REVERT: L 6 LYS cc_start: 0.8728 (tttm) cc_final: 0.8013 (pttm) REVERT: M 447 GLU cc_start: 0.8369 (mp0) cc_final: 0.7687 (mt-10) outliers start: 22 outliers final: 12 residues processed: 120 average time/residue: 0.1430 time to fit residues: 25.0387 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 : 0.491 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 90 THR 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 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: 20.0000 chunk 120 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.052767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.035813 restraints weight = 128486.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.036622 restraints weight = 62375.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.037114 restraints weight = 41096.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.037386 restraints weight = 32840.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.037520 restraints weight = 29307.896| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16874 Z= 0.215 Angle : 0.593 10.907 24363 Z= 0.347 Chirality : 0.034 0.151 2742 Planarity : 0.004 0.050 1819 Dihedral : 30.258 179.177 5168 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.30 % Allowed : 12.51 % Favored : 85.19 % 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 aren not related in a simple way. whole: 2.62 (0.26), residues: 1025 helix: 2.54 (0.20), residues: 668 sheet: 1.35 (0.79), residues: 49 loop : 0.00 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 82 TYR 0.013 0.002 TYR G 57 PHE 0.019 0.002 PHE L 59 TRP 0.014 0.002 TRP M 498 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00473 (16874) covalent geometry : angle 0.59288 (24363) hydrogen bonds : bond 0.04599 ( 1002) hydrogen bonds : angle 3.48712 ( 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 118 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7693 (mtt) cc_final: 0.7329 (mtt) REVERT: C 91 GLU cc_start: 0.8567 (tp30) cc_final: 0.8323 (tp30) REVERT: D 93 GLU cc_start: 0.8614 (mp0) cc_final: 0.8407 (mp0) REVERT: E 97 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7102 (mt-10) REVERT: H 42 TYR cc_start: 0.8041 (t80) cc_final: 0.7822 (t80) REVERT: K 10 PHE cc_start: 0.6978 (t80) cc_final: 0.6651 (t80) REVERT: K 56 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8475 (tm-30) REVERT: K 82 ARG cc_start: 0.8933 (tmm-80) cc_final: 0.8638 (mmt180) REVERT: L 6 LYS cc_start: 0.8764 (tttm) cc_final: 0.8114 (pttp) REVERT: M 447 GLU cc_start: 0.8427 (mp0) cc_final: 0.7794 (mt-10) outliers start: 20 outliers final: 13 residues processed: 110 average time/residue: 0.1411 time to fit residues: 22.9538 Evaluate side-chains 97 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS 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 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: 10.0000 chunk 83 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3553 r_free = 0.3553 target = 0.052674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036233 restraints weight = 126344.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037023 restraints weight = 60613.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.037528 restraints weight = 39992.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.037794 restraints weight = 31790.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037891 restraints weight = 28404.110| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16874 Z= 0.188 Angle : 0.569 8.991 24363 Z= 0.336 Chirality : 0.033 0.145 2742 Planarity : 0.004 0.043 1819 Dihedral : 30.102 178.060 5168 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.87 % Allowed : 13.55 % Favored : 83.58 % 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 aren not related in a simple way. whole: 2.78 (0.27), residues: 1025 helix: 2.67 (0.20), residues: 668 sheet: 1.34 (0.80), residues: 49 loop : 0.06 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 482 TYR 0.013 0.001 TYR G 57 PHE 0.017 0.001 PHE L 59 TRP 0.011 0.002 TRP M 498 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00410 (16874) covalent geometry : angle 0.56913 (24363) hydrogen bonds : bond 0.04424 ( 1002) hydrogen bonds : angle 3.33707 ( 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 122 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.405 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: 0.8659 (mmm) cc_final: 0.8364 (mmm) REVERT: E 97 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7117 (mt-10) REVERT: H 42 TYR cc_start: 0.7961 (t80) cc_final: 0.7676 (t80) REVERT: K 10 PHE cc_start: 0.6990 (t80) cc_final: 0.6650 (t80) REVERT: K 56 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8574 (tm-30) REVERT: K 82 ARG cc_start: 0.8985 (tmm-80) cc_final: 0.8728 (mmt180) REVERT: L 6 LYS cc_start: 0.8826 (tttm) cc_final: 0.8319 (pttp) REVERT: M 447 GLU cc_start: 0.8397 (mp0) cc_final: 0.7834 (mt-10) REVERT: M 470 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8028 (mmtm) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 0.1374 time to fit residues: 23.0082 Evaluate side-chains 102 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE 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 62 ILE 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 3 THR 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: 9.9990 chunk 89 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.053209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036607 restraints weight = 127326.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.037429 restraints weight = 60727.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.037932 restraints weight = 39741.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.038193 restraints weight = 31622.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038352 restraints weight = 28260.799| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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 = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16874 Z= 0.154 Angle : 0.559 9.926 24363 Z= 0.327 Chirality : 0.033 0.162 2742 Planarity : 0.004 0.041 1819 Dihedral : 29.967 177.957 5167 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.95 % Allowed : 15.84 % 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 aren not related in a simple way. whole: 2.88 (0.27), residues: 1025 helix: 2.78 (0.20), residues: 670 sheet: 0.82 (0.81), residues: 50 loop : 0.09 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 60 TYR 0.014 0.001 TYR L 43 PHE 0.013 0.001 PHE L 59 TRP 0.011 0.001 TRP M 498 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00329 (16874) covalent geometry : angle 0.55942 (24363) hydrogen bonds : bond 0.03772 ( 1002) hydrogen bonds : angle 3.15697 ( 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 115 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.448 Fit side-chains 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: 0.8353 (mmm) REVERT: F 84 MET cc_start: 0.8496 (mmm) cc_final: 0.8292 (mmm) REVERT: F 88 TYR cc_start: 0.8953 (m-10) cc_final: 0.8730 (m-10) REVERT: H 42 TYR cc_start: 0.7838 (t80) cc_final: 0.7585 (t80) REVERT: K 10 PHE cc_start: 0.6993 (t80) cc_final: 0.6560 (t80) REVERT: K 56 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8455 (tm-30) REVERT: K 82 ARG cc_start: 0.9028 (tmm-80) cc_final: 0.8815 (mmt180) REVERT: L 6 LYS cc_start: 0.8801 (tttm) cc_final: 0.8285 (ptpp) REVERT: L 28 GLU cc_start: 0.8692 (pm20) cc_final: 0.8256 (pm20) REVERT: M 444 GLU cc_start: 0.7445 (tp30) cc_final: 0.6437 (tp30) REVERT: M 447 GLU cc_start: 0.8357 (mp0) cc_final: 0.7641 (mt-10) REVERT: M 453 ARG cc_start: 0.9160 (ttm170) cc_final: 0.8842 (ttm110) REVERT: M 482 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8163 (tpp80) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.1512 time to fit residues: 23.6749 Evaluate side-chains 104 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 76 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.051807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035053 restraints weight = 128866.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035828 restraints weight = 64295.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036254 restraints weight = 42882.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036545 restraints weight = 34781.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036673 restraints weight = 31029.864| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 16874 Z= 0.305 Angle : 0.659 9.354 24363 Z= 0.377 Chirality : 0.037 0.198 2742 Planarity : 0.004 0.044 1819 Dihedral : 30.313 177.856 5167 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.99 % Allowed : 16.30 % Favored : 80.71 % 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 aren not related in a simple way. whole: 2.32 (0.26), residues: 1025 helix: 2.31 (0.19), residues: 670 sheet: 1.00 (0.83), residues: 47 loop : -0.07 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 71 TYR 0.018 0.002 TYR B 51 PHE 0.021 0.002 PHE L 49 TRP 0.014 0.002 TRP M 498 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00678 (16874) covalent geometry : angle 0.65895 (24363) hydrogen bonds : bond 0.05979 ( 1002) hydrogen bonds : angle 3.66202 ( 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 112 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8655 (mmm) cc_final: 0.8263 (mmm) REVERT: D 62 MET cc_start: 0.9457 (tpp) cc_final: 0.9238 (tpp) REVERT: E 97 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7209 (mt-10) REVERT: H 42 TYR cc_start: 0.8092 (t80) cc_final: 0.7858 (t80) REVERT: K 10 PHE cc_start: 0.7090 (t80) cc_final: 0.6676 (t80) REVERT: K 56 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8594 (tm-30) REVERT: K 82 ARG cc_start: 0.9004 (tmm-80) cc_final: 0.8781 (mmt180) REVERT: L 6 LYS cc_start: 0.8797 (tttm) cc_final: 0.8321 (ptpp) REVERT: M 482 ARG cc_start: 0.8350 (tpp80) cc_final: 0.8086 (tpp80) outliers start: 26 outliers final: 20 residues processed: 103 average time/residue: 0.1493 time to fit residues: 22.2645 Evaluate side-chains 100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 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 50 ILE 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 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: 9.9990 chunk 130 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 49 optimal weight: 0.0980 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3562 r_free = 0.3562 target = 0.053038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.036709 restraints weight = 126116.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.037509 restraints weight = 61295.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037986 restraints weight = 40384.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.038260 restraints weight = 32292.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.038385 restraints weight = 28858.675| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 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 = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16874 Z= 0.146 Angle : 0.568 9.331 24363 Z= 0.331 Chirality : 0.033 0.209 2742 Planarity : 0.004 0.046 1819 Dihedral : 30.076 177.256 5167 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.95 % Allowed : 17.57 % Favored : 80.48 % 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 aren not related in a simple way. whole: 2.78 (0.26), residues: 1025 helix: 2.71 (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 0.002 0.000 ARG F 78 TYR 0.011 0.001 TYR G 57 PHE 0.020 0.001 PHE L 59 TRP 0.007 0.001 TRP M 498 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00309 (16874) covalent geometry : angle 0.56839 (24363) hydrogen bonds : bond 0.03897 ( 1002) hydrogen bonds : angle 3.19437 ( 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 111 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8666 (mmm) cc_final: 0.8368 (mmm) REVERT: E 97 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7073 (mt-10) REVERT: F 88 TYR cc_start: 0.8924 (m-10) cc_final: 0.8703 (m-10) REVERT: H 42 TYR cc_start: 0.7815 (t80) cc_final: 0.7514 (t80) REVERT: K 10 PHE cc_start: 0.6979 (t80) cc_final: 0.6560 (t80) REVERT: K 56 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8594 (tm-30) REVERT: L 6 LYS cc_start: 0.8754 (tttm) cc_final: 0.8312 (ptpp) REVERT: M 447 GLU cc_start: 0.8485 (mp0) cc_final: 0.7694 (mt-10) REVERT: M 482 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8205 (tpp80) outliers start: 17 outliers final: 16 residues processed: 104 average time/residue: 0.1471 time to fit residues: 22.3267 Evaluate side-chains 94 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.052402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035722 restraints weight = 128576.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.036513 restraints weight = 63384.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.036994 restraints weight = 42110.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037236 restraints weight = 33723.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.037399 restraints weight = 30263.205| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16874 Z= 0.212 Angle : 0.603 9.809 24363 Z= 0.349 Chirality : 0.034 0.215 2742 Planarity : 0.004 0.052 1819 Dihedral : 30.113 177.060 5167 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.41 % Allowed : 17.45 % Favored : 80.14 % 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 aren not related in a simple way. whole: 2.60 (0.26), residues: 1025 helix: 2.58 (0.20), residues: 670 sheet: 1.13 (0.84), residues: 47 loop : -0.11 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 82 TYR 0.013 0.002 TYR G 57 PHE 0.019 0.002 PHE L 49 TRP 0.010 0.001 TRP M 498 HIS 0.005 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00467 (16874) covalent geometry : angle 0.60251 (24363) hydrogen bonds : bond 0.04777 ( 1002) hydrogen bonds : angle 3.38867 ( 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 104 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8673 (mmm) cc_final: 0.8350 (mmm) REVERT: E 97 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7143 (mt-10) REVERT: H 42 TYR cc_start: 0.7953 (t80) cc_final: 0.7665 (t80) REVERT: K 10 PHE cc_start: 0.7149 (t80) cc_final: 0.6742 (t80) REVERT: K 56 GLU cc_start: 0.8645 (tm-30) cc_final: 0.7305 (mp0) REVERT: K 57 ASP cc_start: 0.9389 (t0) cc_final: 0.8868 (t70) REVERT: L 6 LYS cc_start: 0.8722 (tttm) cc_final: 0.8192 (ptpp) REVERT: L 56 GLU cc_start: 0.8369 (tt0) cc_final: 0.7807 (pm20) REVERT: M 447 GLU cc_start: 0.8468 (mp0) cc_final: 0.7662 (mt-10) REVERT: M 482 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8193 (tpp80) outliers start: 21 outliers final: 19 residues processed: 96 average time/residue: 0.1483 time to fit residues: 21.0579 Evaluate side-chains 100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 46 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 50 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 85 ASP 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 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: 0.9990 chunk 34 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3551 r_free = 0.3551 target = 0.052731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036123 restraints weight = 127007.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.036920 restraints weight = 62431.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037394 restraints weight = 41445.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037663 restraints weight = 33187.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.037772 restraints weight = 29673.553| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16874 Z= 0.174 Angle : 0.584 9.438 24363 Z= 0.337 Chirality : 0.033 0.215 2742 Planarity : 0.004 0.048 1819 Dihedral : 30.056 176.836 5167 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.30 % Allowed : 17.34 % Favored : 80.37 % 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 aren not related in a simple way. whole: 2.72 (0.26), residues: 1025 helix: 2.69 (0.20), residues: 670 sheet: 1.38 (0.87), residues: 45 loop : -0.14 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 82 TYR 0.012 0.001 TYR G 57 PHE 0.019 0.001 PHE L 59 TRP 0.010 0.001 TRP K 84 HIS 0.004 0.001 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00381 (16874) covalent geometry : angle 0.58388 (24363) hydrogen bonds : bond 0.04074 ( 1002) hydrogen bonds : angle 3.27888 ( 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 105 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8693 (mmm) cc_final: 0.8408 (mmm) REVERT: E 97 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7103 (mt-10) REVERT: H 42 TYR cc_start: 0.7879 (t80) cc_final: 0.7597 (t80) REVERT: K 10 PHE cc_start: 0.7103 (t80) cc_final: 0.6745 (t80) REVERT: K 56 GLU cc_start: 0.8624 (tm-30) cc_final: 0.7285 (mp0) REVERT: K 57 ASP cc_start: 0.9331 (t0) cc_final: 0.8801 (t70) REVERT: L 6 LYS cc_start: 0.8721 (tttm) cc_final: 0.8229 (ptpp) REVERT: L 56 GLU cc_start: 0.8493 (tt0) cc_final: 0.7989 (pm20) REVERT: M 447 GLU cc_start: 0.8458 (mp0) cc_final: 0.7672 (mt-10) REVERT: M 482 ARG cc_start: 0.8443 (tpp80) cc_final: 0.8202 (tpp80) outliers start: 20 outliers final: 17 residues processed: 97 average time/residue: 0.1510 time to fit residues: 21.3699 Evaluate side-chains 100 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE 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 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: 5.9990 chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 0.0010 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 79 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.053621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.037153 restraints weight = 127631.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.037976 restraints weight = 61625.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038473 restraints weight = 40470.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038727 restraints weight = 32251.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038895 restraints weight = 28877.654| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16874 Z= 0.140 Angle : 0.567 9.294 24363 Z= 0.329 Chirality : 0.033 0.213 2742 Planarity : 0.004 0.050 1819 Dihedral : 29.809 175.908 5167 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.38 % Allowed : 18.48 % Favored : 80.14 % 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 aren not related in a simple way. whole: 2.90 (0.27), residues: 1025 helix: 2.79 (0.20), residues: 672 sheet: 1.34 (0.87), residues: 47 loop : -0.00 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 82 TYR 0.010 0.001 TYR G 57 PHE 0.018 0.001 PHE L 49 TRP 0.017 0.001 TRP K 84 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00296 (16874) covalent geometry : angle 0.56713 (24363) hydrogen bonds : bond 0.03440 ( 1002) hydrogen bonds : angle 3.07698 ( 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 107 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 88 TYR cc_start: 0.8878 (m-10) cc_final: 0.8673 (m-10) REVERT: H 42 TYR cc_start: 0.7741 (t80) cc_final: 0.7443 (t80) REVERT: H 93 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: K 10 PHE cc_start: 0.7237 (t80) cc_final: 0.6847 (t80) REVERT: K 56 GLU cc_start: 0.8697 (tm-30) cc_final: 0.7433 (mp0) REVERT: K 57 ASP cc_start: 0.9332 (t0) cc_final: 0.8793 (t70) REVERT: L 6 LYS cc_start: 0.8718 (tttm) cc_final: 0.8336 (ptpp) REVERT: M 447 GLU cc_start: 0.8496 (mp0) cc_final: 0.7584 (mt-10) REVERT: M 482 ARG cc_start: 0.8497 (tpp80) cc_final: 0.8256 (tpp80) outliers start: 12 outliers final: 11 residues processed: 104 average time/residue: 0.1437 time to fit residues: 22.1399 Evaluate side-chains 96 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 78 PHE 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: 5.9990 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN M 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.051874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035178 restraints weight = 129634.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035966 restraints weight = 64121.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036435 restraints weight = 42622.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036675 restraints weight = 34130.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.036837 restraints weight = 30608.854| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16874 Z= 0.299 Angle : 0.683 15.437 24363 Z= 0.383 Chirality : 0.037 0.217 2742 Planarity : 0.005 0.051 1819 Dihedral : 30.290 177.014 5167 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.18 % Allowed : 18.25 % Favored : 79.56 % 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 aren not related in a simple way. whole: 2.40 (0.26), residues: 1025 helix: 2.39 (0.19), residues: 671 sheet: 1.14 (0.86), residues: 47 loop : -0.15 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 60 TYR 0.015 0.002 TYR A 99 PHE 0.016 0.002 PHE L 49 TRP 0.011 0.002 TRP M 498 HIS 0.006 0.002 HIS L 7 Details of bonding type rmsd covalent geometry : bond 0.00664 (16874) covalent geometry : angle 0.68255 (24363) hydrogen bonds : bond 0.05689 ( 1002) hydrogen bonds : angle 3.62482 ( 2493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3140.84 seconds wall clock time: 54 minutes 49.98 seconds (3289.98 seconds total)